Enhanced sample processing devices, systems and methods

ABSTRACT

Devices, systems, and methods for processing sample materials. The sample materials may be located in a plurality of process chambers in the device, which is rotated during heating of the sample materials.

RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.10/840,766, filed May 6, 2004 now U.S. Pat. No. 6,987,253 which is adivisional application of U.S. patent application Ser. No. 09/894,810,filed Jun. 28, 2001 (now U.S. Pat. No. 6,734,401), which claims thebenefit of U.S. Provisional Patent Application Ser. No. 60/214,508 filedon Jun. 28, 2000 and titled THERMAL PROCESSING DEVICES AND METHODS; U.S.Provisional Patent Application Ser. No. 60/214,642 filed on Jun. 28,2000 and titled SAMPLE PROCESSING DEVICES, SYSTEMS AND METHODS; U.S.Provisional Patent Application Ser. No. 60/237,151 filed on Oct. 2, 2000and titled SAMPLE PROCESSING DEVICES, SYSTEMS AND METHODS; U.S.Provisional Patent Application Ser. No. 60/260,063 filed on Jan. 6, 2001and titled SAMPLE PROCESSING DEVICES, SYSTEMS AND METHODS; and U.S.Provisional Patent Application Ser. No. 60/284,637 filed on Apr. 18,2001 and titled ENHANCED SAMPLE PROCESSING DEVICES, SYSTEMS ANDMETHODS—all of which are hereby incorporated by reference in theirentireties.

GRANT INFORMATION

The present invention may have been made with support from the U.S.Government under NIST Grant No. 70NANB8H4002. The U.S. Government mayhave certain rights in the inventions recited herein.

TECHNICAL FIELD

The present invention relates to devices, methods and systems forprocessing of sample materials, such as methods used to amplify geneticmaterials, etc.

BACKGROUND

Many different chemical, biochemical, and other reactions are sensitiveto temperature variations. Examples of thermal processes in the area ofgenetic amplification include, but are not limited to, Polymerase ChainReaction (PCR), Sanger sequencing, etc. The reactions may be enhanced orinhibited based on the temperatures of the materials involved. Althoughit may be possible to process samples individually and obtain accuratesample-to-sample results, individual processing can be time-consumingand expensive.

One approach to reducing the time and cost of thermally processingmultiple samples is to use a device including multiple chambers in whichdifferent portions of one sample or different samples can be processedsimultaneously. When multiple reactions are performed in differentchambers, however, one significant problem can be accurate control ofchamber-to-chamber temperature uniformity. Temperature variationsbetween chambers may result in misleading or inaccurate results. In somereactions, for example, it may be critical to control chamber-to-chambertemperatures within the range of ±1° C. or less to obtain accurateresults.

The need for accurate temperature control may manifest itself as theneed to maintain a desired temperature in each of the chambers, or itmay involve a change in temperature, e.g., raising or lowering thetemperature in each of the chambers to a desired setpoint. In reactionsinvolving a change in temperature, the speed or rate at which thetemperature changes in each of the chambers may also pose a problem. Forexample, slow temperature transitions may be problematic if unwantedside reactions occur at intermediate temperatures. Alternatively,temperature transitions that are too rapid may cause other problems. Asa result, another problem that may be encountered is comparablechamber-to-chamber temperature transition rate.

In addition to chamber-to-chamber temperature uniformity and comparablechamber-to-chamber temperature transition rate, another problem may beencountered in those reactions in which thermal cycling is required isoverall speed of the entire process. For example, multiple transitionsbetween upper and lower temperatures may be required. Alternatively, avariety of transitions (upward and/or downward) between three or moredesired temperatures may be required. In some reactions, e.g.,polymerase chain reaction (PCR), thermal cycling must be repeated up tothirty or more times. Thermal cycling devices and methods that attemptto address the problems of chamber-to-chamber temperature uniformity andcomparable chamber-to-chamber temperature transition rates, however,typically suffer from a lack of overall speed—resulting in extendedprocessing times that ultimately raise the cost of the procedures.

One or more of the above problems may be implicated in a variety ofchemical, biochemical and other processes. Examples of some reactionsthat may require accurate chamber-to-chamber temperature control,comparable temperature transition rates, and/or rapid transitionsbetween temperatures include, e.g., the manipulation of nucleic acidsamples to assist in the deciphering of the genetic code. See, e.g., T.Maniatis et al. Molecular Cloning, A Laboratory Manual, Cold SpringHarbor Laboratory (1982). Nucleic acid manipulation techniques includeamplification methods such as polymerase chain reaction (PCR); targetpolynucleotide amplification methods such as self-sustained sequencereplication (3SR) and strand-displacement amplification (SDA); methodsbased on amplification of a signal attached to the targetpolynucleotide, such as “branched chain” DNA amplification; methodsbased on amplification of probe DNA, such as ligase chain reaction (LCR)and QB replicase amplification (QBR); transcription-based methods, suchas ligation activated transcription (LAT) and nucleic acidsequence-based amplification (NASBA); and various other amplificationmethods, such as repair chain reaction (RCR) and cycling probe reaction(CPR). Other examples of nucleic acid manipulation techniques include,e.g., Sanger sequencing, ligand-binding assays, etc.

One common example of a reaction in which all of the problems discussedabove may be implicated is PCR amplification. Traditional thermalcycling equipment for conducting PCR uses polymeric microcuvettes thatare individually inserted into bores in a metal block. The sampletemperatures are then cycled between low and high temperatures, e.g.,55° C. and 95° C. for PCR processes. When using the traditionalequipment according to the traditional methods, the high thermal mass ofthe thermal cycling equipment (which typically includes the metal blockand a heated cover block) and the relatively low thermal conductivity ofthe polymeric materials used for the microcuvettes result in processesthat can require two, three, or more hours to complete for a typical PCRamplification.

One attempt at addressing the relatively long thermal cycling times inPCR amplification involves the use of a device integrating 96 microwellsand distribution channels on a single polymeric card. Integrating 96microwells in a single card does address the issues related toindividually loading each sample cuvette into the thermal block. Thisapproach does not, however, address the thermal cycling issues such asthe high thermal mass of the metal block and heated cover or therelatively low thermal conductivity of the polymeric materials used toform the card. In addition, the thermal mass of the integrating cardstructure can extend thermal cycling times. Another potential problem ofthis approach is that if the card containing the sample wells is notseated precisely on the metal block, uneven well-to-well temperaturescan be experienced, causing inaccurate test results.

Yet another problem that may be experienced in many of these approachesis that the volume of sample material may be limited and/or the cost ofthe reagents to be used in connection with the sample materials may alsobe limited and/or expensive. As a result, there is a desire to use smallvolumes of sample materials and associated reagents. When using smallvolumes of these materials, however, additional problems related to theloss of sample material and/or reagent volume through vaporization, etc.may be experienced as the sample materials are, e.g., thermally cycled.

Another problem experienced in the preparation of finished samples(e.g., isolated or purified samples of, e.g., nucleic acid materialssuch as DNA, RNA, etc.) of human, animal, plant, or bacterial originfrom raw sample materials (e.g., blood, tissue, etc.) is the number ofthermal processing steps and other methods that must be performed toobtain the desired end product (e.g., purified nucleic acid materials).In some cases, a number of different thermal processes must beperformed, in addition to filtering and other process steps, to obtainthe desired finished samples. In addition to suffering from the thermalcontrol problems discussed above, all or some of these processes mayrequire the attention of highly skilled professionals and/or expensiveequipment. In addition, the time required to complete all of thedifferent process steps may be days or weeks depending on theavailability of personnel and/or equipment.

One example is in the preparation of a finished sample (e.g., purifiednucleic acid materials) from a starting sample (e.g., a raw sample suchas blood, bacterial lysate, etc.). To obtain a purified sample of thedesired materials in high concentrations, the starting sample must beprepared for, e.g., PCR, after which the PCR process is performed toobtain a desired common PCR reaction product. The common PCR reactionproduct must then be prepared for, e.g., Sanger sequencing, followed byperformance of the Sanger sequencing process. Afterwards, themultiplexed Sanger sequencing product must be demultiplexed. Afterdemultiplexing, the finished Sanger sequencing product is ready forfurther processing. This sequence of events may, however, have occurredover days or even weeks. In addition, the technical nature of theprocesses requires highly skilled personnel to obtain accurate results.

Approaches at using disc-based devices to integrate various thermalprocessing steps into a single device suffer from a number ofdisadvantages including the use of high cost silicon substrates and theincorporation of high cost heating and/or cooling systems built into thediscs. As a result, the cost of the discs can be prohibitive to theirwidespread use. See, e.g., International Publication Nos. WO 98/07019(Kellog et al.); WO 99/09394 (Hubbard et al.).

SUMMARY OF THE INVENTION

The present invention provides devices, systems, and methods forprocessing sample materials. The sample materials may be located in aplurality of process chambers in the device, which is rotated duringheating of the sample materials. The rotation may provide a variety ofadvantages over known sample processing methods, systems, and devices.

One advantage of rotating the device during heating of the samplematerial in the process chambers is that, as the temperature of thesample materials rises and vapor is formed, it typically attempts tomove upstream, i.e., towards the axis of rotation of the device.However, once outside of the process chambers, the vaporized materialstend to condense as they cool. The condensed sample materials arereturned to the sample chambers due to the centrifugal forces providedby the rotation. As a result, rotation during heating helps to retainthe sample materials in the process chambers during heating—an advantagethat may be particularly significant where small volumes of samplematerials and/or reagents are used.

Another advantage may include, e.g., enhanced cooling through convectionas the device rotates during processing. As a result, the cooling ofsample materials may be expedited without relying solely on more complexsystems that include, e.g., Peltier elements, etc. to provide for theremoval of thermal energy from the sample materials.

Another potential advantage of rotating the device while heating thesample material is that control over heating of sample materials in theprocess chambers may be enhanced. For example, increasing the rotationalspeed of the device may improve heating control by essentially dampingthe temperature increase of the sample material (by, e.g., increasingconvective cooling during the heating process). Changing the rotationalspeed of the device may also be used to, e.g., control the amount ofenergy reaching each of the process chambers.

Another potential advantage is that uniformity of sample materialtemperature in the different process chambers may also be improved byrotating the device during heating. For example, where heating isaccomplished by directing electromagnetic energy at thermal structuresin a base plate on which the device is rotating, rotation can be helpfulto, e.g., prevent uneven heating due to hot spots generated by theelectromagnetic energy source.

Other advantages of the devices and methods of the present inventioninclude the ability to perform complex thermal processing on samplematerials in a manner that reduces variability of the results due to,e.g., human error. Further, with respect to the processing of biologicalmaterials for, e.g., genetic amplification, this advantage may beachieved by operators that have a relatively low skill level as comparedto the higher skill level of operators required to perform currentlyused methods.

As discussed above, the thermal control advantages of the devices,methods and systems of the present invention may includechamber-to-chamber temperature uniformity, comparable chamber-to-chambertemperature transition rates, and the increased speed at which thermalenergy can be added or removed from the process chambers. Among thedevice features that can contribute to these thermal control advantagesare the inclusion of a reflective layer (e.g., metallic) in the device,baffle structures to assist in removing thermal energy from the device,and low thermal mass of the device. By including thermal indicatorsand/or absorbers in the devices, enhanced control over chambertemperature may be achieved even as the device is rotated duringprocessing.

In those embodiments that include connected process chambers in whichdifferent processes may be sequentially performed on a starting sample,the present invention may provide an integrated solution to the need forobtaining a desired finished product from a starting sample even thoughmultiple thermal processes are required to obtain the finished product.

In other embodiments in which the process chambers are multiplexed froma loading chamber (in which the starting sample is loaded), it may bepossible to obtain multiple finished samples from a single startingsample. Those multiple finished samples may be the same materials wherethe multiplexed process chambers are designed to provide the samefinished samples. Alternatively, the multiple finished samples may bedifferent samples that are obtained from a single starting sample.

For those embodiments of the devices that include distribution channelsformed in a metallic layer, the ductility of the metallic layer mayprovide a further advantage in that it may be possible to close or crushselected distribution channels to tailor the devices for specific testprotocols, adjust for smaller sample material volumes, etc. It may alsobe advantageous to isolate the process chambers by closing or crushingthe distribution channels after distributing sample materials to theprocess chambers.

For those embodiments that include a reflective layer forming a portionof each of the desired process chambers, the present invention may alsoprovide the advantage of improved signal strength when the samplescontained in the process chambers are monitored for fluorescent or otherelectromagnetic energy signals. The signal strength may be improved ifthe reflective (e.g., metallic) layer reflects the electromagneticenergy being monitored as opposed to absorbing the energy or allowing itto be transmitted away from a detector. The signal strength may be evenfurther improved if the metallic layer is formed into a shape that actsas a focusing reflector (e.g., parabolic reflector). If electromagneticenergy used to interrogate and/or heat materials in the process chambersis reflected by the reflective layer, then that layer may also improvethe efficiency of the interrogation and/heating processes by effectivelydoubling the path length of the electromagnetic energy through thesample materials in the process chambers.

A further advantage of the embodiments of the invention that include ametallic layer is the relatively high strength to thickness ratioprovided by the metallic layer. This may be particularly true whencompared to devices that rely solely on polymeric materials to constructthermal processing devices. In addition to physical strength, themetallic layer may also provide beneficial barrier properties, i.e., aresistance to moisture vapor permeability. Another advantage that mayalso be provided by a metallic layer is its amenability to piercingwithout fracture to either introduce materials into, e.g., a loadingchamber, or to remove materials, e.g., a finished sample, from a processchamber.

An advantage of those embodiments including filter chambers with captureplugs is that filtering material appropriate for the particular processbeing performed may be added at the point-of-use. For example, if thedevice is being used for genetic amplification, a filtering materialdesigned to allow passage of nucleic acid materials of particular sizesmay be delivered to the filter chamber before processing of the geneticmaterials.

Advantages of those embodiments including the valving mechanisms of thepresent invention include the ability to control movement of materialsthrough the array of chambers and passageways present on the devices. Afurther advantage of the preferred valving mechanisms is that they donot contaminate the sample materials (as may, e.g., wax valves). Anotheradvantage of the valving mechanisms may include the ability toselectively open the valves using, e.g., laser energy, while the devicesare rotating during sample processing.

Advantages of those embodiments of the invention that include controlpatterns include the ability to control the delivery of electromagneticenergy to the device or other functions, e.g., detection of changes inthe process chambers, without requiring changes to the hardware and/orsoftware used in the system employing the device. For example, theamount and/or wavelength of electromagnetic energy delivered to theprocess chambers and/or valves can be controlled using a control patternon the device. Such control may further reduce the operator errorassociated with using the devices.

As used in connection with the present invention, “thermal processing”(and variations thereof) means controlling (e.g., maintaining, raising,or lowering) the temperature of sample materials to obtain desiredreactions. As one form of thermal processing, “thermal cycling” (andvariations thereof) means sequentially changing the temperature ofsample materials between two or more temperature setpoints to obtaindesired reactions. Thermal cycling may involve, e.g., cycling betweenlower and upper temperatures, cycling between lower, upper, and at leastone intermediate temperature, etc.

As used in connection with the present invention, the term“electromagnetic energy” (and variations thereof) means electromagneticenergy (regardless of the wavelength/frequency) capable of beingdelivered from a source to a desired location or material in the absenceof physical contact. Nonlimiting examples of electromagnetic energyinclude laser energy, radio-frequency (RF), microwave radiation, lightenergy (including the ultraviolet through infrared spectrum), etc. Itmay be preferred that electromagnetic energy be limited to energyfalling within the spectrum of ultraviolet to infrared radiation(including the visible spectrum).

In one aspect, the present invention provides a method of conducting athermal cycling process by providing a device including a plurality ofprocess chambers, each process chamber of the plurality of processchambers defining a volume for containing sample material; providing abase plate including a top surface, a bottom surface, and a thermalstructure; locating a first major surface of the device in contact withthe top surface of the base plate, wherein at least some processchambers of the plurality of process chambers are in thermalcommunication with the thermal structure when the device is in contactwith the top surface of the base plate; providing sample material in theplurality of process chambers; and controlling the temperature of thethermal structure by directing electromagnetic energy at the bottomsurface of the base plate while rotating the base plate and the deviceabout the axis of rotation, whereby the temperature of the samplematerial is controlled.

In another aspect, the present invention provides a method of conductinga thermal cycling process by providing a device including a plurality ofprocess chambers, each process chamber of the plurality of processchambers defining a volume for containing sample material; providing abase plate including a top surface, a bottom surface, and a thermalstructure that includes at least one thermoelectric module; locating afirst major surface of the device in contact with the top surface of thebase plate, wherein the plurality of process chambers are in thermalcommunication with the thermal structure when the device is in contactwith the top surface of the base plate; providing sample material in theplurality of process chambers; and controlling the temperature of thethermal structure by controlling the temperature of the at least onethermoelectric module while rotating the base plate and the device aboutthe axis of rotation, wherein the temperature of the sample material iscontrolled.

In another aspect, the present invention provides a method of conductinga thermal cycling process by providing a device including a plurality ofprocess chambers, each process chamber of the plurality of processchambers defining a volume for containing sample material; providingsample material in the plurality of process chambers; directingelectromagnetic energy into the plurality of process chambers to raisethe temperature of the sample material in the plurality of processchambers; and rotating the device about an axis of rotation whiledirecting electromagnetic energy into the plurality of process chambers,wherein the temperature of the sample material in the plurality ofprocess chambers is controlled as the device rotates about the axis ofrotation.

In another aspect, the present invention provides a method of processingsample material by providing a device including at least one processchamber array that includes a loading chamber and a first processchamber; providing sample material in the at least one process chamberarray, the sample material being provided in the loading chamber of theat least one process chamber array; moving the sample material from theloading chamber to the first process chamber of the at least one processchamber array by rotating the device the device about an axis ofrotation; providing a base plate including a top surface, a bottomsurface, and a thermal structure; locating a first major surface of thedevice in contact with the top surface of the base plate, wherein thefirst process chamber of the at least one process chamber array is inthermal communication with the thermal structure when the device is incontact with the top surface of the base plate; and controlling thetemperature of the thermal structure by directing electromagnetic energyat the bottom surface of the base plate while rotating the base plateand the device about the axis of rotation, whereby the temperature ofthe sample material is controlled.

In another aspect, the present invention comprises a method ofconducting a thermal cycling process by providing a device including aplurality of process chamber arrays, each process chamber array of theplurality of process chamber arrays including a loading chamber and afirst process chamber; providing a base plate including a top surface, abottom surface, and a thermal structure that includes at least onethermoelectric module; locating a first major surface of the device incontact with the top surface of the base plate, wherein the firstprocess chamber of at least one process chamber array of the pluralityof process chamber arrays is in thermal communication with the thermalstructure when the device is in contact with the top surface of the baseplate; providing sample material in at least one process chamber arrayof the plurality of process chamber arrays, the sample material beingprovided in the loading chamber of the at least one process chamberarray; moving the sample material from the loading chamber to the firstprocess chamber of the at least one process chamber array by rotatingthe device the device about an axis of rotation; and controlling thetemperature of the thermal structure by controlling the temperature ofthe at least one thermoelectric module while rotating the base plate andthe device about the axis of rotation, wherein the temperature of thesample material is controlled.

In another aspect, the present invention provides a method of processingsample material by providing a device including a plurality of processchamber arrays, each process chamber array of the plurality of processchamber arrays including a loading chamber and a first process chamber;providing sample material in at least one process chamber array of theplurality of process chamber arrays, the sample material being providedin the loading chamber of the at least one process chamber array; movingthe sample material from the loading chamber to the first processchamber of the at least one process chamber array by rotating the devicethe device about an axis of rotation; directing electromagnetic energyinto the first process chamber of the at least one process chamber arrayto raise the temperature of the sample material in the first processchamber of the at least one process chamber array; and rotating thedevice about an axis of rotation while directing electromagnetic energyinto the first process chamber of the at least one process chamberarray, wherein the temperature of the sample material in the firstprocess chamber of the at least one process chamber array is controlledas the device rotates about the axis of rotation.

In another aspect, the present invention provides a device forprocessing sample material, the device including a substrate thatincludes first and second major surfaces; a plurality of processchambers in the device, each of the process chambers defining a volumefor containing a sample; and a plurality of valves with at least one ofthe valves located between selected pairs of the process chambers, eachvalve including an impermeable barrier, wherein the impermeable barrierof each of the valves separates the selected pairs of process chambers.

In another aspect, the present invention provides a device forprocessing sample material, the device including a substrate thatincludes first and second major surfaces; a plurality of processchambers in the device, each of the process chambers defining a volumefor containing a sample; and a plurality of valves with at least one ofthe plurality of valves located between selected pairs of the processchambers, each valve including shape memory polymer.

In another aspect, the present invention provides a device forprocessing sample material, the device including a substrate thatincludes first and second major surfaces; a plurality of processchambers in the device, each of the process chambers defining a volumefor containing a sample; and a seal defining the volume of at least someof the process chambers, wherein the seal comprises shape memorypolymer.

In another aspect, the present invention provides a device forprocessing sample material, the device including a substrate thatincludes first and second major surfaces; a plurality of processchambers in the device, each of the process chambers defining a volumefor containing a sample; and a control pattern on the device, thecontrol pattern including at least one indicator associated with each ofthe plurality of process chambers, each of the indicators having atleast one characteristic indicative of electromagnetic energy to bedelivered to each process chamber associated with that indicator,whereby the delivery of the electromagnetic energy to selected processchambers can be controlled.

In another aspect, the present invention provides a method of processingsample material by providing a device including a plurality of processchamber arrays, each of the process chamber arrays including a loadingchamber and a process chamber; providing sample material in the loadingchamber of at least one of the process chamber arrays; moving the samplematerial from the loading chamber to the process chamber by rotating thedevice; providing paramagnetic particles within the sample materiallocated in the process chamber; providing a magnet proximate the device;and rotating the device such that the paramagnetic particles within thesample material are subjected to the magnetic field of the magnet duringthe rotating.

In another aspect, the present invention provides a sample processingsystem including a rotating base plate; at least one thermal structureattached to the base plate, the at least one thermal structure includinga top surface and a bottom surface; and at least one thermoelectricmodule in thermal communication with the thermal structure, the at leastone thermoelectric module arranged to control the temperature of thethermal structure while the base plate is rotating.

These and other features and advantages of the devices, systems andmethods of the invention are described below with respect toillustrative embodiments of the invention.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a top plan view of one device according to the presentinvention.

FIG. 2 is an enlarged partial cross-sectional view of a process chamberand distribution channel in the device of FIG. 1.

FIG. 3 is an enlarged partial cross-sectional view of an alternatedevice according to the present invention, illustrating a processchamber, distribution channel and a baffle structure.

FIG. 4 is a plan view of one major side of the device of FIG. 3.

FIG. 4A is a schematic diagram of one baffle structure and airflowthrough the structure as a sample processing device is rotated in onedirection.

FIG. 4B is a schematic diagram of the baffle structure of FIG. 4Adepicting airflow when the sample processing device is rotated in theopposite direction.

FIG. 5 is an enlarged partial cross-sectional view of a process chamberand distribution channel in the device of FIG. 3 after isolation of theprocess chamber.

FIG. 6 is a perspective view of a portion of one edge of anotheralternative device according to the present invention.

FIG. 7 is a plan view of a portion of the device of FIG. 6 including aprocess chamber, a distribution channel and baffles.

FIG. 8 is a cross-sectional view taken along line 8—8 in FIG. 7.

FIG. 9 is a schematic diagram of one thermal processing system accordingto the present invention.

FIG. 9A is a plan view of an alternative base plate for a thermalprocessing system according to the present invention.

FIG. 9B is a cross-sectional view of the base plate of FIG. 9A with asample processing device 310′ located thereon.

FIG. 9C is a plan view of an alternative base plate for a thermalprocessing system according to the present invention.

FIG. 10 is partial cross-sectional view of another device according tothe present invention.

FIG. 10A depicts one device according to the present invention thatincludes temperature sensing material on the device.

FIG. 11 is a partial cross-sectional view of another device according tothe present invention.

FIG. 12 is a schematic diagram of another thermal processing systemaccording to the present invention.

FIG. 13 is a partial cross-sectional view of another device according tothe present invention taken along line 13—13 in FIG. 14.

FIG. 14 is a plan view of one surface of a device according to thepresent invention.

FIG. 15 is a partial cross-sectional view of the device of FIGS. 13 and14 taken along line 15—15 in FIG. 16.

FIG. 16 is a plan view of another surface of the device of FIGS. 13–15.

FIG. 17 is a schematic diagram of one structure that may be used toprovide integrated processing of starting sample materials by, e.g., PCRamplification and Sanger sequencing on a single device.

FIG. 18 is a plan view of one major surface of a device according to thepresent invention.

FIG. 19 is a cross-sectional view of the device of FIG. 18 taken alongline 19—19 in FIG. 18.

FIG. 19A is a plan view of an alternative loading chamber design for usein connection with the present invention.

FIG. 19B is an enlarged cross-sectional view of the loading chamber ofFIG. 19A taken along line 19B—19B in FIG. 19A.

FIG. 19C is a cross-sectional view of a seal system that may be used inconnection with the process chambers of the present invention.

FIG. 19D is a cross-sectional view of a probe accessing the interior ofthe process chamber through the seal system of FIG. 19C.

FIG. 20 is a plan view of the other major surface of the device of FIG.18, depicting a control pattern provided on the device.

FIG. 21 is a cross-sectional view of another device according to thepresent invention.

FIG. 22 is a cross-sectional view of the device of FIG. 21 after openingof one of the valves in the device.

FIGS. 23A & 23B depict an alternative valve structure for use inconnection with the devices and methods of the present invention.

FIGS. 24A & 24B depict an alternative valve structure for use inconnection with the devices and methods of the present invention.

FIGS. 25A & 25B depict an alternative valve structure for use inconnection with the devices and methods of the present invention.

FIG. 26 depicts an alternative seal system for use in connection withthe devices and methods of the present invention.

FIG. 27 depicts another sample processing device of the presentinvention.

FIG. 28 is a side view of the sample processing device of FIG. 27 with amagnet located proximate the device.

FIGS. 29 & 30 depict an alternative process chamber constructionincluding an expansion chamber to assist with mixing of materials in theprocess chamber.

FIGS. 31 & 32 depict another alternative process chamber constructionfor use in devices according to the present invention.

FIG. 33 depicts the process chamber construction of FIGS. 31 & 32 inconjunction with a mating base plate protrusion for use in connectionwith the present invention.

DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS OF THE INVENTION

The present invention provides a device that can be used in methods thatinvolve thermal processing, e.g., sensitive chemical processes such asPCR amplification, ligase chain reaction (LCR), self-sustaining sequencereplication, enzyme kinetic studies, homogeneous ligand binding assays,and more complex biochemical or other processes that require precisethermal control and/or rapid thermal variations. The device may include,e.g., a reflective layer, baffle structures, valve structures, captureplugs, thermal indicators, absorptive materials, and other materials orcomponents that facilitate rapid and accurate thermal processing ofsample materials in the process chambers of the device.

Although construction of a variety of illustrative embodiments ofdevices are described below, rotatable sample processing devicesaccording to the principles of the present invention may be manufacturedaccording to the principles described in U.S. Provisional PatentApplication Ser. No. 60/214,508 filed on Jun. 28, 2000 and titledTHERMAL PROCESSING DEVICES AND METHODS; U.S. Provisional PatentApplication Ser. No. 60/214,642 filed on Jun. 28, 2000 and titled SAMPLEPROCESSING DEVICES, SYSTEMS AND METHODS; U.S. Provisional PatentApplication Ser. No. 60/237,072 filed on Oct. 2, 2000 and titled SAMPLEPROCESSING DEVICES, SYSTEMS AND METHODS; and U.S. Provisional PatentApplication Ser. No. 60/284,637 filed on Apr. 18, 2001 and titledENHANCED SAMPLE PROCESSING DEVICES, SYSTEMS AND METHODS. Other potentialdevice constructions may be found in, e.g., U.S. Pat. No. 6,627,159 andtitled CENTRIFUGAL FILLING OF SAMPLE PROCESSING DEVICES and U.S.Provisional Patent Application Ser. No. 60/260,063 filed on Jan. 6, 2001and titled SAMPLE PROCESSING DEVICES, SYSTEMS AND METHODS.

Although relative positional terms such as “top” and “bottom” may beused in connection with the present invention, it should be understoodthat those terms are used in their relative sense only. For example,when used in connection with the devices of the present invention, “top”and “bottom” are used to signify opposing sides of the devices. Inactual use, elements described as “top” or “bottom” may be found in anyorientation or location and should not be considered as limiting themethods, systems, and devices to any particular orientation or location.For example, the top surface of the device may actually be located belowthe bottom surface of the device in use (although it would still befound on the opposite side of the device from the bottom surface).

One illustrative device manufactured according to the principles of thepresent invention is depicted in FIGS. 1 and 2. The device 10 ispreferably in the shape of a circular disc as illustrated in FIG. 1,although any other shape that can be rotated could be used in place ofthe preferred circular disc. The device 10 of FIGS. 1 and 2 is amulti-layered composite structure including a substrate 20, first layer30, and a second layer 40.

The device 10 includes a plurality of process chambers 50, each of whichdefines a volume for containing a sample and any other materials thatare to be thermally cycled with the sample. The illustrated device 10includes ninety-six process chambers 50, although it will be understoodthat the exact number of process chambers provided in connection with adevice manufactured according to the present invention may be greaterthan or less than ninety-six, as desired.

The process chambers 50 in the illustrative device 10 are in the form ofchambers, although the process chambers in devices of the presentinvention may be provided in the form of capillaries, passageways,channels, grooves, or any other suitably defined volume.

It is preferred that the substrate 20, first layer 30 and second layer40 of the device 10 be attached or bonded together with sufficientstrength to resist the expansive forces that may develop within theprocess chambers 50 as, e.g., the constituents located therein arerapidly heated during thermal processing. The robustness of the bondsbetween the components may be particularly important if the device 10 isto be used for thermal cycling processes, e.g., PCR amplification. Therepetitive heating and cooling involved in such thermal cycling may posemore severe demands on the bond between the sides of the device 10.Another potential issue addressed by a more robust bond between thecomponents is any difference in the coefficients of thermal expansion ofthe different materials used to manufacture the components.

Also disclosed in FIG. 2 is a reagent 52 located within the processchamber 50. The reagent 52 may preferably be fixed to a surface of theprocess chamber 50. The reagent 52 is optional, i.e., some devices 10may or may not include any reagents 52 loaded in the process chambers50. In another variation, some of the process chambers 50 may include areagent 52 while others do not. In yet another variation, differentprocess chambers 50 may contain different reagents.

The illustrated device 10 also includes an optional registration system,whereby the position of the different process chambers 50 can beaccurately determined, even as the device 10 is rotated during theprocessing methods described in more detail below. The registrationsystem may be provided in the form of registration marks 14 on thedevice 10. Another alternative registration system may involve keyingthe device 10 such that it can be mounted on, e.g., a rotating spindle,in only one orientation. In such a system, the rotational position ofthe spindle would then be indicative of the position of the variousfeatures on the device 10. Other registration systems will be known tothose skilled in the art.

The process chambers 50 are in fluid communication with distributionchannels 60 that, together with loading chamber 62, provide adistribution system for distributing samples to the process chambers 50.Introduction of samples into the device 10 through the loading chamber62 may be accomplished by rotating the device 10 about a central axis ofrotation such that the sample materials are moved outwardly due tocentrifugal forces generated during rotation. Before the device 10 isrotated, the sample can be introduced into the loading chamber 62 fordelivery to the process chambers 50 through distribution channels 60.The process chambers 50 and/or distribution channels 60 may includeports through which air can escape and/or other features to assist indistribution of the sample materials to the process chambers 50.Alternatively, sample materials could be loaded into the processchambers 50 under the assistance of vacuum or pressure.

Alternatively, the distribution system used to deliver sample materialsto the process chambers 50 may be “unvented.” As used in connection withthe present invention, an “unvented distribution system” is adistribution system (i.e., process chamber array) in which the onlyopenings leading into the volume of the distribution channels 60 and theprocess chambers 50 are located in the loading chamber 62. In otherwords, to reach the process chamber 50 within an unvented distributionsystem, sample materials must be delivered to the loading chamber 62.Similarly, any air or other fluid located within the distribution systembefore loading with sample material must also escape from thedistribution system through the loading chamber 62. In contrast, avented distribution system would include at least one opening outside ofthe loading chamber. That opening would allow for the escape of any airor other fluid located within the distribution system before loadingduring distribution of the sample material to the process chambers 50.

Moving sample material through within sample processing devices 10 thatinclude unvented distribution systems may be facilitated by alternatelyaccelerating and decelerating the device 10 during rotation, essentiallyburping the sample materials through the channels 60 and into processchambers 50. The rotating may be performed using at least twoacceleration/deceleration cycles, i.e., an initial acceleration,followed by deceleration, second round of acceleration, and second roundof deceleration.

It may further be helpful if the acceleration and/or deceleration arerapid. The rotation may also preferably only be in one direction, i.e.,it may not be necessary to reverse the direction of rotation during theloading process. Such a loading process allows sample materials todisplace the air in those portions of the system that are locatedfarther from the center of rotation of the device 10 than the openinginto the system. One advantage of an unvented distribution system, i.e.,a distribution system including at least some channels and processchambers outside (radially) of any vents, is that leakage from thosevents is prevented.

The actual acceleration and deceleration rates may vary based on avariety of factors such as temperature, size of the device, distance ofthe sample material from the axis of rotation, materials used tomanufacture the devices, properties of the sample materials (e.g.,viscosity), etc. One example of a useful acceleration/decelerationprocess may include an initial acceleration to about 4000 revolutionsper minute (rpm), followed by deceleration to about 1000 rpm over aperiod of about 1 second, with oscillations in rotational speed of thedevice between 1000 rpm and 4000 rpm at 1 second intervals until thesample materials have traveled the desired distance.

The distribution channel 60 illustrated in FIG. 2 is formed in thesubstrate 20 of the illustrative device 10. The channel 60 is in fluidcommunication with the process chamber 50 and is also in fluidcommunication with the loading chamber 62. The channel 60 may be formedby a variety of techniques, preferably a microreplication technique.Examples of suitable microreplication techniques include micromilling,injection molding, vacuum molding, laser ablation, photolithography,thermoforming, embossing, etc.

The illustrated device 10 includes a loading chamber 62 with twosubchambers 64 that are isolated from each other. As a result, adifferent sample can be introduced into each subchamber 64 for loadinginto the process chambers 50 that are in fluid communication with therespective subchamber 64 of the loading chamber 62 through distributionchannels 60. It will be understood that the loading chamber 62 maycontain only one chamber or that any desired number of subchambers 64,i.e., two or more subchambers 64, could be provided in connection withthe device 10.

FIG. 2 is an enlarged cross-sectional view of a portion of the device 10including one of the process chambers 50 and a distribution channel 60.The substrate 20 includes a first major side 22 and a second major side24. Each of the process chambers 50 is formed, at least in part in thisembodiment, by a void 26 formed through the substrate 20. Theillustrated void 26 is formed through the first and second major sides22 and 24 of the substrate 20.

The substrate 20 is preferably polymeric, but may be made of othermaterials such as glass, silicon, quartz, ceramics, etc. Furthermore,although the substrate 20 is depicted as a homogenous, one-pieceintegral body, it may alternatively be provided as a non-homogenous bodyof, e.g., layers of the same or different materials. For those devices10 in which the substrate 20 will be in direct contact with the samplematerials, it may be preferred that the material or materials used forthe substrate 20 be non-reactive with the sample materials. Examples ofsome suitable polymeric materials that could be used for the substratein many different bioanalytical applications may include, but are notlimited to, polycarbonate, polypropylene (e.g., isotacticpolypropylene), polyethylene, polyester, etc.

A first layer 30 is provided on one side of the substrate 20 in theillustrated embodiment and preferably includes a metallic sub-layer 34located between an optional passivation layer 32 and an optional outerprotective layer 36. The first layer 30 thus defines a portion of thevolume of the process chamber 50. A second layer 40 is provided on theopposite side of the substrate 20 to define the remainder of the volumeof the process chamber 50.

It may be preferred that at least a portion of the materials definingthe volume of the process chamber 50 be transmissive to electromagneticenergy of selected wavelengths. The selected wavelengths may bedetermined by a variety of factors, for example, electromagnetic energydesigned to heat and/or interrogate a sample in the process chamber 50,electromagnetic energy emitted by the sample (e.g., fluorescence), etc.

In the device 10, where the first layer 30 includes a metallic sub-layer34, it may be preferred that the materials used for the second layer 40of the device 10 transmit electromagnetic energy of selectedwavelengths. By providing a transmissive process chamber 50, a sample inthe chamber can be interrogated by electromagnetic energy of selectedwavelengths (if desired) and/or electromagnetic energy of the selectedwavelengths emanating from the sample can be transmitted out of theprocess chamber 50 where it can be detected by suitable techniques andequipment. For example, electromagnetic energy may be emittedspontaneously or in response to external excitation. A transmissiveprocess chamber 50 may also be monitored using other detectiontechniques, such as color changes or other indicators of activity orchanges within the process chambers 50.

In some instances, however, it may be desirable to prevent thetransmission of selected wavelengths of electromagnetic energy into theprocess chambers. For example, it may be preferred to prevent thetransmission of electromagnetic energy in the ultraviolet spectrum intothe process chamber where that energy may adversely impact any reagents,sample materials, etc. located within the process chamber.

In the device illustrated in FIG. 2, the first layer 30 preferablyincludes a structure such that the first layer 30 deviates from anotherwise flat surface on at least the surface 37 facing the interiorvolume of the process chamber 50. For example, the first layer 30 may becast, molded, thermoformed, embossed or otherwise manufactured toproduce an interior surface 37 that has a desired shape. The shape ofthe structure formed in the first layer 30 may vary, although it may bepreferred that the shape of the interior surface 37 facing the volume ofthe process chamber 50 be concave (e.g., parabolic) such that somefocusing of any electromagnetic energy reflected from that surface maybe effected.

It may also be preferred that the exterior surface of the first layer30, i.e., the surface that faces away from the substrate 20, alsoinclude baffle structure 38 such that airflow is disrupted over thefirst layer 30 as the device 10 is rotated. By disrupting airflow overthe first layer 30, heat transfer of energy out of the first layer 30into the surrounding atmosphere may be enhanced. The illustrated firstlayer 30 includes a baffle structure 38 with a shape that corresponds tothe shape of the interior surface 37 of the metallic sub-layer 34,although the shape of the baffle structure 38 may, alternatively, bedifferent than the shape of the interior surface 37.

The metallic sub-layer 34 is preferably not exposed to the interiorvolume of the process chamber 50 to prevent contamination of any sampleby the metal or metals used in the metallic sub-layer 34. The optionalpassivation layer 32 is provided to prevent exposure of the metallicsub-layer 34 to the interior volume of the process chamber 50. Thematerials used in the passivation layer 32 are preferably capable ofsecure attachment to both the metallic sub-layer 34 and the materialsused in for the substrate 20 by, e.g., adhesives, heat sealing, etc. Itis also preferred that the materials used for the passivation layer 32be non-reactive with any materials in the samples located within theprocess chambers 50. Examples of suitable materials for the passivationlayer 32 may include, but are not limited to, thermoplastics,polypropylene (e.g., isotactic polypropylene), polyethylene, polyester,etc.

Although the passivation layer 32 is depicted as a single homogenousstructure, it may be formed as two or more layers of the same ordifferent materials. For example, an adhesion promoting layer may beused to enhance adhesion of the passivation layer 32 to, e.g., themetallic sub-layer 34. The adhesion promoting layer may be, e.g.,heat-sealable, a pressure sensitive adhesive, hot melt adhesive, curableadhesive, etc.

Further, although the passivation layer 32 is preferably substantiallycoextensive with the metallic sub-layer 34, the passivation layer 32 maybe provided in a discontinuous pattern on the metallic sub-layer 34,with the discontinuous pattern preventing exposure of the metallicsub-layer 34 to the interiors of the process chambers 50.

The materials and/or thickness of the passivation layer 32 may alsopreferably be selected to transmit electromagnetic energy of selectedwavelengths to allow for reflection from the underlying metallicsub-layer 34 without significant absorption or diffusion. This may beparticularly true where the shape of the interior surface of themetallic sub-layer 34 is designed to provide some focusing ofelectromagnetic energy. It may also be preferred that the passivationlayer 32 be relatively thin so that the transfer of thermal energy fromany sample materials in the process chambers 50 into the metallicsub-layer 34 is not substantially inhibited (so that energy can bedissipated into the atmosphere or another structure). For example, wherethe passivation layer 32 is an isotactic polypropylene, the layer 32 maypreferably be about 0.005 inches (0.13 mm) or less, more preferablyabout 0.002 inches (0.05 mm) or less.

The metallic sub-layer 34 may take a variety of forms. Although thelayer 34 is depicted as a single, homogenous structure, it may beprovided as a multi-layer structure of two or more layers. It may bepreferred that the metallic sub-layer 34 consist essentially of one ormore metals. Examples of suitable metals that could be used in themetallic sub-layer 34 include aluminum, stainless steel, copper,titanium, silver, gold, tin, etc. One potential advantage of a metallicsub-layer 34 is that the metallic layer may assist in equilibrating thetemperature between process chambers 50 by conducting heat away from hotspots or into cool spots on the device 10.

The thickness of the layer 34 may be selected to provide a relativelylow thermal mass to facilitate rapid thermal cycling of the samples inthe process chambers 50. The desire for low thermal mass of the metallicsub-layer 34 may, however, be balanced by a number of factors.

For example, the desire for a metallic sub-layer 34 with low thermalmass may be balanced by a desire for thermal conductivity across thedevice 10, e.g., between chambers 50. That thermal conductivity acrossthe device 10 can contribute to chamber-to-chamber temperatureuniformity, as well as comparable chamber-to-chamber temperaturetransition rate.

Another factor to balance with the desire for reduced thermal mass isthe need for integrity of the first layer 30. In many devices 10, themetallic sub-layer 34 may provide a significant portion, or even amajority, of the structural integrity of the first layer 30. A metallicsub-layer 34 that is too thin or manufactured of the wrong metal ormetals may not provide sufficient integrity for the device 10. Forexample, if the metallic sub-layer 34 is to be formed (e.g., stamped,etc.) to assist in the formation of the process chambers 50,distribution channels (see, e.g., FIG. 3), baffle structure 38, etc.,the metal or metals and their thickness should be amenable to suchprocesses.

The barrier properties of the metal or metals and their thickness usedin the metallic sub-layer 34 may also need to be balanced against thedesire for reduced thermal mass. For example, the metallic sub-layer 34may need to be thick enough to provide sufficient vapor barrierproperties in response to the thermal processing taking place in theprocess chambers 50 or to increase the shelf-life of the device 10where, e.g., moisture sensitive reagents 52 are pre-loaded within theprocess chambers 50.

Yet another factor to consider when selecting the thickness of themetallic sub-layer 34 and the metal or metals in it may be the need forreflectivity. If the metallic sub-layer is too thin and/or formed of thewrong metals, it may not exhibit sufficient reflectivity over theselected wavelengths of electromagnetic energy.

When balancing all of the concerns discussed above, it may be preferredthat the thickness of the metallic sub-layer 34 be about 0.04 inches (1mm) or less, more preferably about 0.02inches (0.5 mm) or less, andstill more preferably about 0.010 inches (0.25 mm) or less. At the lowerend of the range, the thickness of the metallic sub-layer 34 maypreferably be sufficient to provide the desired reflectivity and/orstructural integrity to the first layer 30 of the device 10. Forexample, it may be preferred that the metallic sub-layer 34 be at leastabout 0.0005 inches (0.013 mm) thick, more preferably at least about0.001 inches (0.025 mm) thick, and still more preferably about 0.003inches (0.075 mm).

The actual range of suitable thickness for the metallic sub-layer 34 maydepend, at least in part, on the thermal properties of the metal ormetals used to form the layer. Where the layer 34 is formed of aluminum,the layer 34 may preferably have a thickness in the range of, e.g.,about 0.025 millimeters (mm) to about 0.25 mm.

As an alternative, the reflective properties desired in the devices ofthe present invention may be provided by non-metallic reflectivematerials. For example, multi-layer polymeric films may be used toprovide the desired reflectivity or to enhance the reflectivity ofmetallic layers used in the devices of the present invention. Reflectivepolymeric films that may be useful in connection with the presentinvention are described in U.S. Pat. No. 5,882,774 (Jonza et al.); U.S.Pat. No. 6,101,032 (Wortman et al.); and International Publication Nos.WO 99/36809, WO 99/36810, WO 99/36812, WO 99/36248, and WO 99/36258.

Also depicted in FIG. 2 is an optional protective layer 36 provided onthe surface of the metallic sub-layer 34 that faces away from theprocess chamber 50. The protective layer 36 may protect the integrity ofthe metallic sub-layer 34 and/or may increase the toughness of thedevice 10. Another potential advantage of the protective layer 36 is thereduction or prevention of oxidation of the metallic sub-layer 34 (whichcould adversely affect the rate of thermal energy transfer out of themetallic sub-layer 34).

Still another advantage of providing both an outer protective layer onone side of a metallic sub-layer and a passivation layer on the otherside of the metallic layer is that the formability of the first layer 30may be improved. If, for example, a side of the device including ametallic sub-layer 34 is to be formed to provide process chambers (see,e.g., FIG. 3), distribution channels, baffle structures, or any otherfeatures, the formability of the side including the metallic sub-layermay be improved if the metallic sub-layer is covered on both sides. Thismay be especially true with forming processes that involve molding(e.g., plug molding, vacuum molding, thermoforming, etc.).

The thickness and the materials used for the protective layer 36 arepreferably such that the layer 36 does not substantially affect thetransfer of thermal energy out of the metallic sub-layer 34. An exampleof one suitable protective layer 36 is a thin coating of epoxy with athickness of about 0.001 inches (0.025mm). Other examples ofnon-metallic protective layer materials include, but are not limited to,polyester, polycarbonate, polypropylene, polyethylene, etc.

One product that may meet many of the above criteria for the first layer30 is a heat sealing metal foil available from Marsh BiomedicalProducts, Inc., Rochester New York under the designation AB-0559.

FIG. 3 is an enlarged partial cross-sectional view of anotherillustrative embodiment of a device 110 according to the presentinvention, the second layer 140 of which is illustrated in the plan viewprovided in FIG. 4. The device 110 includes a substrate 120, first layer130 and second layer 140 constructed in much the same manner as thedevice 10 described above. It should be noted that the first layer 130of the device 110 does not include the optional outer protective layerof device 10, but is preferably constructed of a passivation layer 132and a metallic sub-layer 134.

Among the other differences between the device 10 and device 110 arethat the distribution channel 160 that is in fluid communication withthe process chamber 150 is formed primarily as a structure in the firstlayer 130. The structure required to form the channel 160 in the firstlayer 130 can also provide a baffle structure 138 on the bottom of thedevice 110. The baffles 138 formed in the bottom layer 130 could take onthe form of the distribution channels 160 required to distribute samplematerials to the process chambers 150. One example of such a pattern isillustrated by the channels 60 in FIG. 1.

Another difference is that the second layer 140 may also include bafflestructures 142 designed to increase the turbulence in airflow over thedevice 110 as it is rotated. The baffles 142 are seen in FIGS. 3 and 4.Although the illustrated baffles 142 on the cover layer 140 are arrangedradially on the device 110, it will be recognized that they could beprovided in any pattern designed to increase turbulent flow or otherflow that improves heat transfer out of the device 110. The baffles 142may be integral with the second layer 140 or they may be provided asseparate articles adhered or otherwise attached to the second layer 140.

One variation on the baffle structures discussed thus far in connectionwith devices of the present invention is depicted in FIGS. 4A & 4B.Rather than induce turbulent airflow over substantially the entiresurface of the devices, it may be desirable to provide controlledairflow over selected portions of the device 110′. That selected portionmay preferably include, e.g., a process chamber 150′ as illustrated inFIGS. 4A & 4B. In some embodiments, it may be preferred to provide someor all of the process chambers 150′ with an individual baffle structure138′.

In contrast to providing structures that increase turbulent flow oversubstantially the entire surface of the device, the baffle structure138′ depicted in FIGS. 4A & 4B may offer more control over airflow inselected areas. Where a large number of baffle structures 138′ areprovided, the end result may, however, still be turbulent flow oversubstantially the entire surface of the device.

The baffle structure 138′ is directional, i.e., when the device 110′ ismoved in the direction of arrow 139′, airflow is diverted over and/oraround the process chamber 150′ by a fairing 141′ and diverters 142′. Asa result, the baffle structure 138′ may create a pool of relativelystagnant air over the process chamber 150′, thereby potentiallyimproving the speed with which the process chamber 150′ may heated to adesired temperature.

When the device 110′ is rotated in the opposite direction as indicatedby arrow 139″ in FIG. 4B, airflow over the process chamber 150′ may beenhanced as the diverters 142′ operate to capture or scoop air anddirect it over the process chamber 150′. The baffle structure 138′ mayenhance convective air cooling of the process chamber 150′ when rotatedin direction 139″, which is opposite the direction 139′ of FIG. 4A. Thatenhanced convective cooling provides for increased thermal energytransfer out of the process chamber 150′ as compared to devices rotatedwithout the directional baffle structure.

The fairing 141′ may preferably include a narrow leading edge whenrotated in direction 139″ to enhance airflow over the process chamber150′. Many alternative structures may be used in place of those depictedin FIGS. 4A & 4B. For example, the relatively aerodynamic shape of thefairing 141′ may be replaced by, e.g., one or more posts or otherstructures that may be less aerodynamic, but effective to create thedesired pool of stagnant air over process chamber 150′. Likewise, thediverters 142′ may be provided in any suitable form that provides thedesired protection from airflow in one direction and concentration ofairflow in the opposite direction.

FIG. 5 is another enlarged partial cross-sectional view of the device110 of FIGS. 3 and 4. This figure illustrates one technique for sealingor isolating the process chamber 150 to, e.g., preventcross-contamination or diffusion between process chambers 150 in thedevice 110 after the process chambers 150 have been loaded with samplematerial. The illustrated technique involves closing the channel 160 bycompressing the first layer 130 against the substrate 120. The sealingof the channel 160 may be accomplished mechanically, i.e., by simplycrushing the channel 160, or it may be accompanied by the application ofheat to enhance adhesion of the first layer 130 to the substrate 120.Alternatively, sufficient isolation may be achieved by continuouslyrotating the device during processing, such that the sample materialsare retained in the process chambers by centrifugal forces.

The sealing of distribution channels may be performed for a variety ofpurposes in addition to isolating process chambers after distribution ofsample materials. For example, selected distribution channels may besealed before distribution of sample material to reduce the volume ofsample material needed to fill the process chambers that remain in fluidcommunication with the distribution system. In another approach, thetests to be performed using the devices may be customized by sealingselected distribution channels before distributing the sample materialsinto the process chambers.

FIGS. 6–8 depict yet another illustrative embodiment of a device 210manufactured according to the present invention. The device 210 includesa substrate 220, first layer 230 and second layer 240. FIG. 6, aperspective view of a portion of one edge of the device 210, illustratesa baffle 238 provided in the first layer 230 and a baffle 242 in thesecond layer 240. As a result, both major sides of the device 210include at least one baffle, preferably two or more baffles, to increaseturbulent flow over those surfaces.

Referring to FIG. 7, a plan view of a portion of the device 210including a process chamber 250 and a distribution channel 260 in fluidcommunication with the process chamber 250. FIG. 8 is a cross-sectionalview taken along line 8—8 in FIG. 7, and illustrates the process chamber250 and distribution channel 260, both of which are formed in thesubstrate 220 by any suitable technique, preferably a microreplicationtechnique. Examples of suitable microreplication techniques includemicromilling, injection molding, vacuum molding, laser ablation,photolithography, thermoforming, embossing, etc. The process chamber 250is formed primarily by a void formed through the substrate 220.Alternatively, the process chamber 250 may be formed by a depressionformed through only a portion of the thickness of the substrate 220.

The first layer 230 of the device 210 may or may not include any metalsor metallic sub-layers as discussed in connection with the devices 10and 110 above. Also illustrated in FIG. 8 are a baffle 238 on the firstlayer 230 and a baffle 242 on the second layer 240.

One illustrative system for accomplishing a thermal cycling processusing a device according to the present invention is schematicallydepicted in FIG. 9. The system 300 includes a device 310 located on aspindle 314 that rotates the device about an axis 312. The deviceincludes process chambers 350 into which a sample material isdistributed by, e.g., distribution channels as discussed above or anyother suitable techniques and/or structures.

After distribution of the sample material into the process chambers,individual chambers 350 can be selectively heated by suitableelectromagnetic energy supplied by an electromagnetic energy source 370that heats the materials in the process chambers 350. Theelectromagnetic energy source 370 is preferably remote from the device310, i.e., it is not located on the device 310. Examples of somesuitable electromagnetic energy sources may include, but are not limitedto, lasers, broadband electromagnetic energy sources (e.g., whitelight), etc. The electromagnetic energy source 370 may provideelectromagnetic energy continuously or intermittently based on a varietyof factors, e.g., the desired temperature of the sample materials, therate at which thermal energy is removed from each process chamber, thedesired rate of temperature change, whether the process chambers includea reflective component, etc. If the electromagnetic energy source 370 iscycled or otherwise varied, the registration system discussed above maybe used to deliver a selected amount of electromagnetic energy toselected process chambers.

As the device 310 rotates, it is preferred that the airflow over thesurface of the device 310 assists in cooling the sample materials in theprocess chambers 350 to a selected base temperature from the uppertarget temperature to which the sample materials are heated by theelectromagnetic energy from the source 370. In some systems, one or bothsurfaces of the device 310 may be exposed to the atmosphere to alsoassist in cooling. The system 300, however, includes an optional baseplate 380 that may be held at a lower temperature. By holding the bottomof the device 310 in contact with the base plate 380, it may be possibleto assist in cooling the sample materials in the process chambers 350between heating cycles as the device 310 rotates during processing. If abase plate 380 is used to assist in thermal control, it may be helpfulto use a device 310 incorporating a metallic layer proximate the baseplate 380 to improve thermal conductivity between the base plate and thedevice 310.

In other systems, it may be desirable to promote both heating andcooling of the process chambers through the base plate 380. For example,heating and cooling may be facilitated by incorporating thermoelectricmodules (e.g., Peltier elements, resistive heaters, etc.) in the baseplate 380 underneath each of the process chambers 350. A thermoelectricmodule may be provided in the form of a ring located beneath the processchambers 350 or a number of individual thermoelectric modules may beused in connection with base plate 380. The heating of process chambers350 using base plate 380 may be performed in connection with heatingusing electromagnetic energy source 370 to provide even faster heatingand/or more uniform temperature distribution of the process chambers350. Thus, the control over sample material temperature may beaccomplished by simultaneously delivering electromagnetic energy to theprocess chambers 350 and controlling the temperature of thermoelectricmodules above which the process chambers 350 are located.

The system 300 depicted in FIG. 9 also includes an optional additionaltemperature control mechanism in the form of a fluid source 382, e.g.,pressurized air or any other suitable fluid, that can be directed at thesurface of the device 310. The fluid used can be either heated or cooledto a desired temperature. Where it is desired to cycle the samplematerials between upper and lower temperatures, the fluid may beprovided at the lower temperature. Although depicted as being directedat only one surface of the device 310, it will be understood that thefluid may be directed at both surfaces of the device if desired.

The system 300 may also include various other components such as adetection system 390 provided to detect the results of processing of thesample materials in the process chambers 350. For example, the detectionsystem and method may involve active interrogation of the processchambers 350 to detect fluorescent reaction products in the chambers asthe device 310 rotates. The detection may be qualitative orquantitative. Other detection systems may be provided to monitor, e.g.,the temperatures or other properties of the materials in the processchambers 350.

As the thermal cycling method is performed, the temperature within theprocess chambers 350 may be monitored to control the application ofenergy into the chambers 350. Among the variables that may bemanipulated to control the sample material temperatures in the device310 include the intensity of the laser or other light source, therotational speed of the device 310 (which can affect the cooling rateand the dwell time of each of the process chambers in the laser or otherlight source), the temperature of the base plate 380 (or any componentssuch as thermoelectric modules located in the base plate 380), and thetemperature and pressure of the fluid source 382.

If the device 310 includes an unvented distribution system, anotheradvantage of rotating the device 310 during heating is that, as thetemperature of the sample materials rises and vapor is formed, it musttravel upstream, i.e., towards the axis of rotation of the device 310(where the only opening into the distribution system is located). Onceoutside of the chamber 350, however, the thermal energy dissipates,causing the vapors to condense. The condensed sample materials are thenreturned to the sample chambers 350 due to the centrifugal forcesprovided by the rotation. The end result is that the sample materialsare, for the most part, retained in the process chambers 350, evenduring rapid heating that may cause some vaporization.

FIGS. 9A and 9B depict an alternative base plate 380′ that includes atleast one thermal structure 384′ that may preferably be constructed of amaterial that absorbs electromagnetic energy. The thermal structures384′ are in thermal communication with at least some of the processchambers of device 310′ (see FIG. 9B) such that heating or cooling ofthe thermal structures 384′ can cause corresponding temperaturevariations in those process chambers. In the depicted embodiment, thethermal structures 384′ are located in contact with the bottom surfaceof the device 310′ and at least some of the process chambers containedtherein.

The thermal structures 384′ may preferably be heated by anelectromagnetic energy source 370′ that, in the depicted embodiment, islocated on the opposite side of the thermal structures 384′ from thedevice 310′. The electromagnetic energy source 370′ directselectromagnetic energy at the bottom surface of the thermal structures384′. The thermal structures 384′ absorb at least some of theelectromagnetic energy from source 370′ and convert that electromagneticenergy into thermal energy (such that the temperature of the thermalstructure 384′ increases). The thermal energy in thermal structure 384′is transferred between the device 310′ and the thermal structures 384′primarily by conduction.

Although base plate 380′ is depicted with two thermal structures 384′,it will be understood that the base plate 380′ could include any numberof thermal structures 384′ necessary to transfer thermal energy to orfrom the selected process chambers in a device 310′. Further, it may bepreferred that, where more than one thermal structure 384′ is provided,the thermal structures 384′ be independent of each other such that nosignificant amount of thermal energy is transferred between thedifferent independent thermal structures 384′.

The electromagnetic energy source 370′ may be in a form that provideselectromagnetic energy to only one thermal structure 384′ at a time, orit may be capable of heating two or more thermal structures 384′simultaneously. If heating of different thermal structures 384′ atdifferent times is desired, it may be desirable to provide a separateelectromagnetic energy source 370′ dedicated to each thermal structure384′, to move a single energy source 370′ such that it is positionedfacing the thermal structure 384′ to be heated, to provide a shutteringsystem that provides electromagnetic energy to the necessary thermalstructure 384′ at the selected time, etc.

The thermal structures 384′ may be constructed of a variety ofmaterials, provided the materials possess sufficient thermalconductivity and absorb electromagnetic energy generated by theelectromagnetic source 370′ at sufficient rates. In addition, it mayalso be desirable that the material or materials used for the thermalstructures 384′ have sufficient heat capacity to provide a heatcapacitance effect. Examples include, but are not limited to: aluminum,copper, gold, etc. If the thermal structures 384′ are constructed ofmaterials that do not, themselves, absorb electromagnetic energy at asufficient rate, it may be preferred that the thermal structures 384′include a material that improves energy absorption. Fore example, thethermal structures 384′ may be coated with an electromagnetic energyabsorptive material such as carbon black, polypyrrole, inks, etc.

One potential advantage of using thermal structures 384′ in conjunctionwith the electromagnetic source 370′ is that compatibility between theelectromagnetic energy source and any reagents or other materialslocated within the process chambers of the device 310′ may be improved.The thermal structures 384′ may preferably be opaque to theelectromagnetic energy produced by source 370′. As a result, materialswithin the process chambers may be substantially shielded from directexposure to the electromagnetic energy that could, in some instances, bedetrimental to the desired reactions.

Although the thermal structures 384′ are depicted as being located onthe top surface of a sub-plate 386′, it will be understood that anysuitable design that incorporates thermal structures 384′ could be used.For example, the thermal structures 384′ could be embedded in thesub-plate 386′ or no sub-plate 386′ could be provided (with the thermalstructures 384′ interconnected by, e.g., a series of radial struts orother structures). Where a sub-plate 386′ is used, however, it maypreferably be transmissive to the electromagnetic energy, such that theelectromagnetic energy is able to reach the thermal structures 384′ toprovide the desired thermal heating effect.

Alternatively, the sub-plate 386′ may include openings that exposeselected portions of the thermal structures 384′ to the electromagneticenergy provided by electromagnetic energy source 370′. Where thesub-plate 386′ includes openings to expose the bottom surface of thethermal structures 384′, the materials of the sub-plate 386′ may beopaque to the electromagnetic radiation from the electromagnetic source370′.

It may further be desirable that the thermal structures 384′ berelatively thermally isolated from the sub-plate 386′ such that onlylimited amounts (if any) of the thermal energy in the thermal structures384′ is transferred to the sub-plate 386′. That thermal isolation may beachieved, for example, by manufacturing the sub-plate 386′ of materialsthat absorb only limited amounts of thermal energy, e.g. polymers, etc.

The base plate 380′ may also optionally include sensors to detect thetemperature of the thermal structures 384′. FIGS. 9A and 9B depict twosensors 388′ located in contact with the thermal structures 384′ andinformation from the sensors 388′ may be used to control the amount ofenergy provided by the electromagnetic energy source 370′ or to controlthe rate and/or duration of rotation of the base plate 380′ as a part ofany system control over both heating and cooling of the thermalstructures 384′. Alternatively, the thermal structure temperature or thetemperature within the process chambers on device 310′ may be monitoredremotely by, e.g., infrared emissions, etc.

Although the base plate 380′ of FIGS. 9A and 9B includes thermalstructures 384′ in the form of substantially continuous circular rings,the thermal structures 384′ may alternatively be provided as a series ofdiscontinuous thermal elements, e.g., circles, squares, located beneathprocess chambers on the device 310′ that are to be heated by conduction.One advantage, however, of a continuous ring thermal structure is thattemperature of each thermal structure 384′ may equilibrate duringheating, thereby potentially improving chamber-to-chamber temperatureuniformity for all process chambers located above the continuous thermalstructure.

Methods of using the base plate 380′ will, in many aspects, be similarto the use of system 300 described above, with the addition of theelectromagnetic source 370′ directed at the thermal structures 384′ inthe base plate 380′. The energy provided by the electromagnetic energysource 370′ may be controlled to obtain the desired temperatures in theprocess chambers (by, e.g. varying the power output of the source 370′,providing a shutter system, etc.).

The heating of process chambers using thermal structures 384′ in baseplate 380′ may be performed in connection with heating using anelectromagnetic energy source located above the device 31 O′ to provideeven faster heating and/or more uniform temperature distribution of theprocess chambers in the device 310′. In such a system and method,electromagnetic radiation may be delivered directly to the processchambers (referring to the system and method depicted in FIG. 9) whilethe process chambers are simultaneously being heated by thermal energyconduction from below using thermal structures 384′. In anotheralternative, the process chambers in the device 310′ may be heated usingonly the thermal structures 384′, i.e., without the need to direct anyelectromagnetic energy directly into the process chambers using, e.g.,an electromagnetic energy source 370 located above the device 310′.

In yet another variation depicted in FIG. 9C, the bottom of a base plate380″ is depicted. A series of openings 383″ are provided in the bottomof the base plate 380″ with the openings 383″ being separated by struts385″. The bottom surface of a thermal structure 384″ is exposed withinthe openings 383″ such that electromagnetic energy directed at thethermal structure 384″ can be absorbed and converted to thermal energyas described above.

Also seen in FIG. 9C are thermoelectric modules 388″ either attached toor embedded within the thermal structure 384″. The thermoelectricmodules 388″ may be provided in the form of, e.g., Peltier elements,resistive heaters, etc. Although a number of thermoelectric modules 388″are depicted, a single thermoelectric module may alternatively beprovided.

With the base plate 380″, control over the temperature of the thermalstructures 384′ may be effected by controlling the temperature of thethermoelectric modules 388″ alone or in combination with electromagneticenergy directed at the bottom surface of the thermal structures 384′.Where the temperature of the thermal structure 384″ is to be controlledby controlling the temperature of the thermoelectric modules 388″ alone(i.e., where the thermal structure 384″ is not to be heated byconverting electromagnetic energy directed at the bottom surface of thethermal structure 384″ to thermal energy), the materials selected formanufacturing the thermal structure 384″ may be chosen based on theirthermal conductivity, with no consideration given for the ability of thematerials to absorb electromagnetic energy. Suitable materials mayinclude but are not limited to, e.g., metals (such as, e.g., aluminum,gold, copper, etc.).

By combining the thermoelectric modules 388″ with the thermal structure384″ advantages may be obtained in the form of improved temperatureuniformity as the thermal structure 384″ serves as a sink to equilibratevariations in the operating characteristics of the individualthermoelectric modules 388″.

The thermoelectric modules 388″ provide another option in controllingthe temperature of sample materials in the process chambers of devicelocated above the thermal structure 384″. The thermoelectric modules388″ may be used in addition to directing electromagnetic energy intothe process chambers and directing electromagnetic energy at the thermalstructure 384″ to provide three heat sources. Alternatively, thethermoelectric modules 388″ may be used alone to heat the processchambers on a device located above the base plate 380″ or they may beused in connection with the delivery of electromagnetic energy directlyinto the process chambers of the device (in the absence ofelectromagnetic energy directed at the bottom surface of the thermalstructure 384″.

The net result is a system having the ability to provide electromagneticenergy directly into the process chambers, thermal structures that canconvert impinging electromagnetic energy into thermal energy forconduction to the process chambers in a device, and thermoelectricmodules whose temperature can be controlled to control the temperatureof the thermal structures (and, in turn, any process chambers in thermalcommunication with the thermal structures). As a result, temperaturecontrol over sample materials within the process chambers of a devicelocated on the base plate may be effected in a variety of manners.

Referring now to FIG. 10, which depicts a partial cross-sectional viewof an alternative device 410 according to the present invention,temperature sensing materials 454 may be located within the processchambers 450 of the device 410. Among the potential temperature sensingmaterials 454 are structures that incorporate thermochromic dyes,temperature-sensitive fluorescent materials, liquid crystal materialswith a colorimetric phase transition, etc. It may be desirable thatthese materials be in direct contact with any sample materials in theprocess chambers 450 and, in the illustrated embodiment, the temperaturesensing material 454 surrounds at least a portion of the process chamber450. Many other structures and techniques for providing such temperaturesensing materials 454 may, however, be substituted for that illustratedin FIG. 10. For example a portion of the substrate 420 or the firstlayer 430 may be doped or coated with a temperature sensing material.

The use of another potential temperature sensing material is depicted inFIG. 10A, where liquid crystal materials (in this example provided inthe form of a film) are provided to supply temperature feedbackinformation. Some liquid crystal materials are available that haverelatively narrow colorimetric phase transition windows of, e.g., 2degrees Centigrade. Such narrow transition window temperature sensorscould be used, e.g., to monitor selected low and high temperatures in athermal processing system. Other liquid crystal materials with broadertransition windows may be monitored for their color change in betweenthe upper and lower limit indicators. One potential advantage of liquidcrystal materials is that their exhibited color changes can be monitoredremotely, i.e., without contacting the material, by, e.g., detecting thecolor changes using a spectrophotometer.

Films incorporating liquid crystal materials could be located in contactwith the sample materials in a process chamber as discussed above withrespect to FIG. 10 (see reference no. 454). In another alternativedepicted in FIG. 10A, the liquid crystal film 454′ is located on athermal structure 484′ that is located below the process chamber 450′(where the thermal structure 484′ is, e.g., similar in construction tothose described above in connection with FIGS. 9A–9C). In such a system,the film 454′ could be used to verify the accuracy of a non-contacttemperature servo-control system controlling the delivery ofelectromagnetic energy to the thermal structure 484′. For example, a lowtemperature indicator could be used to monitor the selected lowtemperature (e.g., about 50° C. to about 52° C.), a high temperatureindicator could be used to monitor the selected high temperature (e.g.,about 94° C. to about 96° C.), and a broad range indicator (e.g., about50° C. to about 100° C.) could be used to monitor the temperature of thethermal structure 484′ in between the selected low and hightemperatures. One alternative to a broad range indicator could be aseries of narrower indicators interspersed between the low and hightemperature indicators.

The liquid crystal film temperature indicators could be used a solesource of temperature feedback, or they could be used to verify theaccuracy and otherwise calibrate other temperature sensors, such as,e.g., the thermocouples described above.

FIG. 11 illustrates another device 510 (in a partial cross-sectionalview) according to the present invention in which electromagnetic energyreceptive materials 556 are located proximate the process chambers 550.It may be desirable that the electromagnetic energy receptive materials556 be in direct contact with any sample materials in the processchambers 550 and, in the illustrated embodiment, the electromagneticenergy receptive materials 556 surround at least a portion of theprocess chamber 550. Many other structures and techniques for providingelectromagnetic energy receptive materials 556 may, however, besubstituted for that illustrated in FIG. 11. For example a portion ofthe substrate 520 or the first layer 530 may be coated with anelectromagnetic energy receptive material.

The electromagnetic energy receptive material 556 can take a variety offorms, provided that is capable of converting electromagnetic radiationin one form or another to thermal energy. That thermal energy can thenbe communicated to the sample materials in the process chambers 550 by,e.g., conduction. Examples of some suitable materials may include thosedescribed in U.S. Pat. Nos. 5,278,377 (Tsai); U.S. Pat. No. 5,446,270(Chamberlain et al.); U.S. Pat. No. 5,529,708 (Palmgren et al.); andU.S. Pat. No. 5,925,455 (Bruzzone et al.). Thermal processes usingelectromagnetic energy absorptive materials are described in, e.g., U.S.Pat. No. 5,721,123 (Hayes et al.).

The advantage of using an electromagnetic energy receptive material 556is that the sample materials in the device 510 can be heated in theabsence of physical contact with the device 510. For example, if theelectromagnetic energy receptive material 556 is sensitive toradio-frequency (RF) radiation, the device 510 can be rotated such thatthe process chambers 550 are resident within an RF field for sufficienttime to obtain the desired heating. Similar non-contact heating may beobtained with microwave radiation, etc. It will, however, be understoodthat the form in which the electromagnetic radiation is provided shouldbe compatible with the sample materials located within the processchambers 550.

Electromagnetic energy receptive materials may include, e.g., absorbersthat absorb light in the visible, near-infrared (NIR) and far-infraredregion such as dye molecules, carbon dispersions, diamond-like carbon,conducting polymers such as polypyrrole. Absorbers could be made in theform of films coated on the walls of the structure, could beincorporated within microcapsules, could be coated on the surface ofbeads or in the form of foams, or in a structure that has thermalproximity by a coating of such material on the exterior of the chamber,the intervening materials between the chamber being thermallyconducting.

Polycarbonate films, for example, impregnated with an NIR dye or otherabsorber can be prepared by solvent casting. These films could beincorporated into the device either by bonding to the process chamber,or by in situ casting of the film in the process chamber. Anotherpotential embodiment is to use encapsulated absorbing molecules in amatrix such as, but not limited to, microcapsules, hollow beads, etc.,made of polymeric organic or inorganic materials.

Carbon-based systems can also be used as films, for example diamond-likecarbon (DLC). DLC can be deposited by a plasma assisted chemical vapordeposition onto a substrate like polycarbonate. Process chambers could,e.g., be coated with DLC films by a masked procedure to, e.g., producepatterned DLC films.

FIG. 12 schematically illustrates another system 500 in which device 510is located on a spindle 514 that rotates the device about an axis 512.The device 510 includes process chambers 550 into which a samplematerial is distributed by, e.g., distribution channels as discussedabove or any other suitable techniques and/or structures.

After distribution of the sample material into the process chambers,individual chambers 550 can be selectively heated by suitableelectromagnetic energy, e.g., RF, microwave, etc., supplied by anelectromagnetic energy source 570 to heat electromagnetic energyreceptive materials in the device 510. The electromagnetic energyreceptive materials can then communicate the thermal energy to samplematerials in the process chambers 550. The electromagnetic energy source570 may be provided continuously or intermittently as discussed abovewith respect to the system 300 above. Various cooling and detectionmechanisms such as those discussed in connection with system 300 (seeFIG. 9) may also be incorporated into system 500.

FIGS. 13–16 illustrate another embodiment of a device in accord with thepresent invention. Portions of the device 610 are depicted in a varietyof plan and partial cross-sectional views. Generally, the device 610 maypreferably be in the form of a disc similar to that seen in, e.g.,FIG. 1. The device 610 includes a core 620 in which a variety ofstructures are formed. A first cover layer 630 is attached to a firstmajor side 622 of the core 620 and a second cover layer 640 is attachedto a second major side 624 of the core 620. FIGS. 13–16 illustrate oneset of interconnected process chambers and other features that may bereplicated a number of times around the device 610 in a manner similarto the process chambers 50 arrayed about device 10 in FIG. 1. Each setof interconnected process chambers and other features can be describedas forming a process chamber array, with a number of the process chamberarrays arranged generally radially about the device 610.

FIG. 13 is a partial cross-sectional view of a portion of the device 610including one of the process chamber arrays that is taken along line13—13 in FIG. 14, which is a plan view of the second major side 624 ofthe core 620 with the second cover layer 640 removed. FIG. 15 is apartial cross-sectional view of a portion of the device 610 taken alongline 15—15 in FIG. 16, which is a plan view of the first major side 622of the core 620 with the first cover layer 640 removed.

The first cover layer 630 may include multiple sub-layers 632, 634, and636 in the various constructions described above. It may be preferredthat the first cover layer 630 include a reflective sub-layer (e.g.,metallic, polymeric, etc.) as discussed in the embodiments describedabove. The second cover layer 640 may include, e.g., an adhesive 642 anda substrate 644, both of which may be optically clear or otherwisetransmissive to electromagnetic energy of selected wavelengths.

Among the features formed in the core 620 are a loading chamber 662 athat, in the illustrated embodiment, is in the form of an annular ring(only a portion of which is seen in FIGS. 13–16). The loading chamber662 a is in fluid communication with a first or inner process chamber650 a through a channel 660 a. It will typically be preferred that theloading chamber 662 a be located closer to the center of the device 610than the inner process chamber 650 a such that rotation of the device610 about its center causes materials located in the loading chamber 662a to move towards inner process chamber 650 a through channel 660 a.

The core 620 also includes features formed in the first major surface622, such as intermediate process chamber 650 b, which may be anotherchamber in which materials are thermally processed. Alternatively, theintermediate process chamber 650 b may be provided to perform anotherfunction, e.g., filter materials delivered to it from inner processchamber 650 a. The intermediate process chamber 650 b may be in fluidcommunication with a second loading chamber 662 b through channel 660 bthat, in the illustrated embodiment, is formed in the first majorsurface 622 of the core 620.

The inner process chamber 650 a and intermediate process chamber 650 bare connected by a channel 660 c and a via 660 d. The channel 660 cextends from the inner process chamber 650 a to the via 660 d which, inturn, extends to the intermediate process chamber 650 b. The channel 660c and/or via 660 d may preferably include a valve structure locatedbetween the process chambers if precise control over the movement ofmaterials between the inner process chamber 650 a and intermediateprocess chamber 650 b is desired. The valve structure may take a numberof forms, e.g., thermal plugs (e.g., waxes, etc.) or other structuresthat can be opened when desired. Alternatively, the valving may beprovided by varying the rotational speed of the disc to overcome theresistance of materials to move through the channel 660 c and/or via 660d.

The intermediate process chamber 650 b is also connected to the outerprocess chamber 650 c by a via 660 e and channel 660 f in a mannersimilar to that used to connect inner process chamber 650 a andintermediate process chamber 650 b. The via 660 e and/or channel 660 fmay also include a valve structure if so desired.

It is preferred that the process chamber array including chambers 650 a,650 b, and 650 c be arranged generally radially from the center of thedevice 610, i.e., the point about which the device is rotated. As aresult, rotation of the device 610 can be used to move materialssuccessively from inner process chamber 650 a to intermediate processchamber 650 b and, finally, to outer process chamber 650 c. By movingthe materials through the process chambers as desired, selectedprocesses can be performed sequentially within the process chamber arrayon the device 610.

It may be desired that the channels and vias in the device 610 may alsoinclude filters or other structures/materials needed to performfunctions. For example, a porous capture plug 670 may be located withinthe via 660 e. The porous capture plug 670 may advantageously capturefilter materials moving from the loading chamber 662 b to theintermediate process chamber 650 b. For example, it may be desirable todispense filtering material in the form of, e.g., beaded size exclusionsubstances. Such materials may be entrained within a fluid when suppliedto the loading chamber 662 b. When the device 610 is rotated, theentrained beads may be driven to the intermediate process chamber 650 bthrough channel 660 b. The porous capture plug 670 in via 660 e allowsthe fluid carrying the beads to pass but prevents the beads frompassing, thereby capturing them within the process chamber 650 b.

A particular advantage of the porous capture plug 670 used to capturefiltering material within process chamber 650 b is that the filtermaterial dispensed to the chamber 650 b may be selected at thepoint-of-use based on the characteristics of the sample materials beingprocessed. Where the filtering material dispensed to the chamber 650 bis, e.g., size exclusion beads, the properties of the beads may beselected to, e.g., remove the typically shorter PCR primers whileallowing the typically longer PCR products to pass through to the outerprocess chamber 650 c. The sizes of the primers and the PCR products mayvary in each application and the ability to select the appropriate sizeexclusion material for process chamber 650 b may be particularlyadvantageous.

Device of the present invention with process chamber arrays such asthose illustrated in, e.g., FIGS. 13–16, may be used to provideintegrated processing of starting sample materials by, e.g.,amplification of a starting sample material within a process chamberarray on a device. Each of the process chamber arrays include a numberof chambers that are preferably arranged generally radially on a device(such that centrifugal forces can move fluids sequentially from chamberto chamber). The chambers within each of the arrays are in fluidcommunication using channels or other conduits that may, in someembodiments, include valve structures to control the movement asdesired.

One example of an integrated process that can be performed in a processchamber array is schematically illustrated in FIG. 17 where a loadingchamber 762 is provided to receive, e.g., a starting sample material.The array and one illustrative method of using the array will bedescribed below. The illustrative method involves PCR amplification,followed by Sanger sequencing to obtain a desired end product. Thiscombination of processes is, however, intended to be illustrative onlyand should not be construed as limiting the present invention.

Starting sample material, e.g., lysed blood cells, is provided in thechamber 762. A filter 763 is preferably provided to filter the startingsample material as it moves from the loading chamber 762 to the firstprocess chambers 750 a. The filter 763 is, however, optional and may notbe required depending on the properties of the starting sample material.

The first process chambers 750 amay preferably include suitable PCRprimers as supplied, e.g., dried down in each of the chambers 750 a.Each of the chambers 750 a may include the same primer or differentprimers depending on the nature of the investigation being performed onthe starting sample material. One alternative to providing the primersin the process chambers 750 abefore loading the sample is to add asuitable primer to the loading chamber 762 with the starting samplematerial (provided that the primer is capable of passing through thefilter 763, if present).

After locating the starting sample material and any required primers inthe process chambers 750 a, the materials in the process chambers 750aare thermally cycled under conditions suitable for PCR amplification ofthe selected genetic material.

After completion of the PCR amplification process, the materials in eachof the first process chambers 750 amay be moved through another filterchamber 752 a (one filter chamber 752 a for each process chamber 750 a)to remove unwanted materials from the amplified materials, e.g., PCRprimers, unwanted materials in the starting sample that were not removedby filter 763, etc. The filter chambers 752 a may, for example, containsize exclusion substances, such as permeation gels, beads, etc. (e.g.,MicroSpin or Sephadex available from Amersham Pharmacia Biotech AB,Uppsala, Sweden).

After clean-up of the sample materials in the filter chambers 752 a, thefiltered PCR amplification products from each of the first processchambers 750 aare moved into a pair of multiplexed second processchambers 750 b for, e.g., Sanger sequencing of the genetic materialsamplified in the first process chambers 750 athrough appropriate controlof the thermal conditions encountered in second process chambers 750 b.

After the desired processing has been performed in the second processchambers 750 b, the processed material (Sanger sequenced sample materialif that is the process performed in the process chambers 750 b) is movedfrom each of the process chambers 750 b through another set of filterchambers 752 b to remove, e.g., dyes or other unwanted materials fromthe product of the second process chambers 750 b. The filtered productis then moved from the filter chambers 752 b into output chambers 750 cwhere it can be removed.

As with the process chamber arrays illustrated in FIGS. 13–16, it isalso preferred that process chamber arrays such as the array illustratedin FIG. 17 be arranged generally radially on a device such that rotationof the device will move materials from the loading chamber 762 towardsthe output chambers 750 c. More preferably, it is preferred that two ormore of the process chamber arrays illustrated in FIG. 17 be arranged ona single device, with the loading chambers 762 of each array locatedclosest to the axis of rotation such that the materials can be movedthrough the array by centrifugal forces developed during rotation.Alternatively, the arrays may be located on a device that is held in amanner that allows rotation of device containing the array such thatcentrifugal forces move the materials from the loading chamber 762towards the output chambers 750 c. Loading of sample materials intoprocess chambers using centrifugal force is also described, for example,in U.S. Pat. No. 6,627,159 and titled CENTRIFUGAL FILLING OF SAMPLEPROCESSING DEVICES.

A variety of advantages of the integrated process chamber arrayillustrated in FIG. 17 stem from the ability to move from a raw startingsample material to an isolated sequenced product in a single device.Among those advantages are reductions in the number physical transfers(by pipetting, etc.) that can be problematic when working with smallvolumes of materials. Another advantage is that multiple parallelprocesses can be simultaneously performed, providing potentialimprovements in confidence levels regarding the accuracy of the processresults. In addition, there may be an enhanced level of control inensuring that the process chambers see the same conditions with respectto, e.g., thermal cycling, etc.

FIGS. 18–20 illustrate another embodiment of a device and methodsaccording to the present invention incorporating valves separating theprocess chambers within each process chamber array. The illustrateddevice 810 includes a plurality of process chamber arrays in a mannersimilar to that described with respect to the embodiment illustrated inFIGS. 13–16 above. One of the process chamber arrays is depicted in theenlarged cross-sectional view of FIG. 19.

The device 810 includes a first cover layer 830 attached to a firstmajor side 822 of the substrate 820 and a second cover layer 840attached to a second major side 824 of the substrate 820. The substrate820 and cover layers 830 and 840 may be attached by any suitabletechnique or techniques, including, but not limited to, adhesives,welding (chemical and/or thermal), etc.

The device 810 also illustrates one embodiment of a registration systemas discussed above in the form of a number of key slots 814 formed aboutthe periphery of the opening 812 in the center of the device 810. Thekey slots 814 can cooperate with complementary structures formed on,e.g., a spindle, used to rotate the device 810. The key slots 814 can,thus, be used to maintain the rotational position of the device 810 onsuch a spindle. Although multiple key slots 814 are shown, it will beunderstood that only one such slot 814 may be required to fix therotational position of the device 810 on a spindle.

The first cover layer 830 may be homogeneous or it may include multiplesub-layers as described above. It may be preferred that the first coverlayer 830 be reflective for electromagnetic energy of selectedwavelengths as described above. The second cover layer 840 may include,e.g., an adhesive on a carrier layer, both of which may be opticallyclear or otherwise transmissive to electromagnetic energy of selectedwavelengths.

Among the features formed in the substrate 820 are a loading chamber 860that, in the illustrated embodiment, is in the form of an annular ring.Each of the process chamber arrays also include inner or first processchambers 850 a and outer or second process chambers 850 b locatedfurther out radially from a center of the device 810.

The loading chamber 860 is in fluid communication with the inner processchamber 850 a through channel 862. As a result, rotation of the device810 about its center will force sample material to move from the loadingchamber 860 into the first process chamber 850 a where the first thermalprocessing of the sample material may be performed.

The device 810 also includes a valve 870 located between and separatingthe inner and outer process chambers 850 a and 850 b. The valve 870 isnormally closed when the device 810 is supplied to a user to preventmovement of the sample material from the first process chamber 850 ainto the second process chamber 850 b.

The valve 870 may preferably be located within a via 880 that is influid communication with inner process chamber 850 a through channel 882on one side and in fluid communication with the outer process chamber850 b through channel 884 on the opposite side. It may be preferred thatthe via 880 be formed such that it extends between the first and secondmajor surfaces 822 and 824 of the substrate 820 as depicted.

The valve 870 includes an impermeable barrier 872 that prevents fluidsfrom moving between the process chambers 850 a and 850 b when it isintact. The impermeable barrier 872 may preferably be distinct from thesubstrate 820, i.e., it is preferably made of a material that isdifferent than the material used for the substrate 820. By usingdifferent materials for the substrate 820 and the impermeable barrier872, each material can be selected for its desired characteristics.Alternatively, the impermeable barrier may be integral with thesubstrate 820, i.e., made of the same material as the substrate 820. Forexample, the impermeable barrier may simply be molded into the substrate820. If so, it may be coated or impregnated to enhance its ability toabsorb electromagnetic energy.

The impermeable barrier 872 may be made of any suitable material,although it may be preferred that the material of the barrier 872 formvoids without the production of any significant byproducts, waste, etc.that could interfere with the reactions or processes taking place inprocess chambers. A preferred class of materials are pigmented orientedpolymeric films, such as, for example, films used to manufacturecommercially available can liners or bags. A suitable film may be ablack can liner, 1.18 mils thick, available from Himolene Incorporated,of Danbury, Conn. under the designation 406230E.

It may further be preferred that the impermeable barrier 872 of thevalve 870 include material susceptible of absorbing electromagneticenergy of selected wavelengths and converting that energy to heat,resulting in the formation of a void in the impermeable barrier 872. Theabsorptive material may be contained within the impermeable barrier 872or coated on a surface thereof.

The valve 870 illustrated in FIG. 19 also includes an optional permeablesupport 874 located proximate at least one side of the impermeablebarrier 872. The support 874 is permeable to the fluids moving betweenthe process chambers 850 a and 850 b, although it may perform somefiltering functions in addition to supporting the impermeable barrier872. It may be preferred that the support 874 be somewhat resilient toassist in sealing the valve 870 by forcing the impermeable barrier 872against the surfaces in the via 880 with sufficient force to preventfluid passage in ordinary use of the device 810.

It may be preferred that the support 874 be provided in the form of aporous material as illustrated in FIG. 19. The porous support 874 maypreferably be coextensive with the impermeable barrier 872 used in thevalve 870. Alternative forms of the support may include rings, sleeves,or any other structure or material that can support at least a portionof the impermeable barrier 872 in the valve 870.

In some embodiments, it may be desirable that the porous support 874reflect electromagnetic energy of selected wavelengths to assist in theopening of the valve 870 and/or prevent the electromagnetic energy fromreaching any underlying fluids, sample materials, etc.

It may be preferred that the porous support 874 be hydrophobic to reduceor prevent fluid contact with the impermeable barrier 872.Alternatively, it may be preferred that the porous support 874 behydrophilic to promote fluid contact with the impermeable barrier 872 ofthe valve 870.

Examples of suitable materials for a porous support may include, but arenot limited to, porous plugs or membranes, including sinteredpolypropylene and sintered polyethylene plugs or membranes, e.g., suchas those commercially available from Porex Corporation, Fairburn, Ga.The impermeable barrier 872 can also be directly bonded into position(e.g., by a pressure sensitive adhesive, silicone adhesive, epoxyadhesive, thermal welding, etc.) without the need for a supportstructure.

The valve 870 is opened by forming a void in the impermeable barrier872. The void may be formed by electromagnetic energy of any suitablewavelength. It may be preferred that laser energy of a suitablewavelength be used. A potential advantage of using laser energy is thatthe same laser used to heat the materials in the process chambers may beused to form the voids needed to place the process chambers in fluidcommunication with each other.

It may further be desirable to place the impermeable barrier 872 of thevalve 870 within a via 880 as illustrated in FIG. 19. Locating theimpermeable barrier 872 within a via 880 and directing electromagneticenergy of some wavelengths into the via 880 may result in someadvantages in that the walls of the via 880 may reflect and/or focus atleast some of the electromagnetic energy to assist in formation of thevoid in the barrier 872.

FIGS. 19A and 19B depict an alternative loading chamber 860′ that may beused on connection with one or more of the process chamber arrays ofdevice 810. The loading chamber 860′ has a funnel shape that may assistin emptying of the loading chamber as the device 810 is rotated. Thewider end of the funnel shaped loading chamber 860′ is preferablylocated closest to the axis of rotation with the loading chamber 860′tapering in the direction of the channel 862′ that leads to the firstprocess chamber (not shown in FIG. 19A).

The loading chamber 860′ also includes an optional inlet port 864′ andan optional vent 866′. These openings are formed in the second coverlayer 840′. The inlet port 864′ may preferably be tapered to assist inguiding, e.g., a pipette tip, into the volume of the loading chamber860′. The vent 866′ assists in loading of the chamber 860′ by providinga opening through which air can escape as the loading chamber 860′ isloaded through inlet port 864′.

Advantages of the funnel-shaped loading chamber 860′ include controlover fluid entry into the system. The shape of the loading chamber 860′can provide for almost 100% filling while reducing or eliminatingtrapped air. In addition, the shape of the loading chamber 860′ may alsoreduce or prevent premature entry of the sample materials into thechannel 862′.

FIGS. 19C and 19D depict an optional seal system that may be used inconnection with one or more of the process chambers in one or more ofthe process chamber arrays in the device 810. The seal system includesan opening 844′ in the cover layer 840′ covering a process chamber 850′formed, at least in part, by a substrate 820′. The opening 844′ isclosed by a seal 846′ that is attached to the inner surface 842′ of thecover layer 840′ over the opening 844′.

The seal 846′ may be attached to the inner surface 842′ by any suitabletechnique, e.g., adhesives, welding, heat sealing, etc. In the depictedembodiment, the seal 846′ is attached to the inner surface 842′ of thecover layer 840′ by adhesive 848′. That adhesive 848′ may be used toalso attach the cover layer 840′ to the substrate 820′ as depicted inFIGS. 19C and 19D.

Use of the seal system is depicted in FIG. 19D where the tip of a probe849′ is shown forcing the seal 846′ away from attachment to the innersurface 842′ of the cover layer 840′. The probe 849′ can then access theinterior of the process chamber 850′ to add to or remove the samplematerial 858′. Although the probe 849′ is depicted as forcing the seal846′ away from only a portion of the cover layer 840′, it may completelydetach the seal 846′ from the cover layer 840′. It may be preferred thatthe opening 844′ in the cover layer 840′ be tapered as depicted, e.g.,in FIGS. 19C and 19D to assist in guiding the tip of the probe 849′ intothe process chamber 850′. This guiding feature may be especially helpfulfor use in connection with robotic unloading systems.

One potential advantage of the seal system is that the probe 849′ is notrequired to cut any components forming the process chamber 850′ toaccess the interior of the process chamber 850′.

The device 810 includes an optional control pattern depicted in FIG. 20that includes indicators 890 a, 890 b, 892, and 894 useful incontrolling the electromagnetic energy delivered to the process chambersand/or valves. In the illustrated embodiment, the control pattern islocated on the first cover layer 830, although other suitable locationsmay alternatively be used.

The indicators used in the control pattern have at least onecharacteristic indicative of the electromagnetic energy to be deliveredto the associated process chamber and/or valve. The characteristics mayinclude size, shape, color, or any other distinguishing feature that maybe detected and used to control the delivery of electromagnetic energy.In the illustrated embodiment, the primary distinguishingcharacteristics include size and/or shape. It may be preferred that theindicators be detected optically (based on, e.g., contrast with thesurrounding surface of the device 810, sensing of a void formed throughthe device 810, etc.).

The illustrated control pattern includes a first set of indicators 890 aassociated with some of the inner process chambers 850 a and a secondset of indicators 890 b associated with the rest of the inner processchambers 850 a. The difference between the sets of indicators is theirsize, with the indicators 890 a being smaller than the indicators 890 b.That size may be used to control the amount of energy delivered to theprocess chambers associated with each indicator, e.g., the largerindicators 890 b may result in the delivery of more energy to theirassociated process chambers 850 a. Alternatively, the differently sizedindicators 890 a and 890 b may be used to control the wavelength of theelectromagnetic energy delivered to the associated process chambers 850a (with each of the different indicators denoting a different wavelengthof energy). In yet another alternative, both the amount and wavelengthof the energy delivered to each process chamber may vary depending onthe characteristics of the associated indicators.

One potentially desirable method for using indicators 890 a and 890 bbased on their sizes and the rotation of the device 810 is to begindelivery of electromagnetic energy when the leading edge of the relevantindicator passes a detector and ceasing delivery of that energy when thetrailing edge of the same indicator passes the detector. Theelectromagnetic energy may be controlled at its source by cycling or thedelivery may be interrupted by, e.g., a shutter, rotating mirror, orother system.

The indicators 890 a and 890 b are each associated with only one of theprocess chambers 850 a. Indicator 892, however, is associated with allof the valves 870 on the device 810 and can be used to control thedelivery of electromagnetic energy needed to open the valves 870 asdescribed above. In a similar manner, delivery of electromagnetic energyto multiple process chambers 850 a could be effected with one indicatorin some systems.

Indicators 894 are associated with the outer process chambers 850 b andcan be used to control delivery of electromagnetic energy to thoseprocess chambers. As illustrated, the shape of the indicators 894 isdifferent from the other indicators and those different characteristicsmay be used for control purposes.

Although the indicators in the illustrated control pattern are locatedgenerally in registration with the process chamber or valve with whichthey are associated, the control pattern need not be so provided. Forexample, the control pattern may occupy only a portion of the surface ofthe device 810, e.g., an outer annular ring.

In another alternative, the control pattern or portions thereof may beused to control other components of a system using the device 810. Forexample, indicators may be provided that control the type of detectorsused to monitor the process chambers for, e.g., a desired product,temperature, pH, etc. Such indicators may be provided in the form of barcodes.

FIGS. 21 and 22 illustrate another construction of a device 910. Thedevice is similar in many respects the device 810. One difference,however, is that the substrate 920 includes an upper layer 920 a and alower layer 920 b with a valve layer 976 located between the upper layer920 a and lower layer 920 b. The valve layer 976 forms the impermeablediscs 972 a and 972 b of the valves 970 a and 970 b. Unlike theimpermeable discs 872 of the valves 870 of the device 810 (which areseparate and distinct from each other), the impermeable discs 972 a and972 b are formed of portions of the same valve layer 976 which extendsbetween the different valves 970 a and 970 b.

The layers 920 a, 920 b and valve layer 976 may be attached together byany suitable technique or combination of techniques. For example, theymay be adhesively attached, welded (thermally, chemically, etc.),heat-sealed, etc. It may be desirable that the valve layer 976 be usedto form the impermeable discs of all of the valves on the device 910 oronly some of the valves. If the valve layer 976 is used to form theimpermeable discs of all of the valves, it may be desirable that thevalve layer 976 be coextensive with the major surfaces of the device910. The laminated construction of the device 910 may provide advantagesin the manufacturing of the devices 910 by allowing the use of web orother continuous manufacturing processes.

The valves 970 a and 970 b are used to separate the process chambers 950a, 950 b and 950 c and control movement of the sample material 958between the chambers. As illustrated in FIG. 21, the sample material 958is located in process chamber 950 a which is not in fluid communicationwith process chamber 950 b due to the closed state of the valve 970 a.

In FIG. 22, however, the impermeable barrier 972 a of valve 970 aincludes a void 973 formed therein after delivery of the appropriateelectromagnetic energy 975 into the via 980 containing the valve 970.That void allow the sample material 958 to move into the process chamber950 b from process chamber 950 a. In the illustrated embodiment, processchamber 950 b includes filter material 959 through which the samplematerial 958 passes on its way to process chamber 950 c.

Such a device could be used in a method of removing ions (e.g.,chloride, phosphate) and/or dyes (e.g., dideoxy nucleotide triphosphatedye terminators (ddNTP), fluorescent dyes, near-infrared dyes, visibledyes) from a biological sample material, as well as other devicesdesigned for moving sample materials from one chamber to another. Themethod includes: providing a device that includes at least two connectedprocess chambers wherein the connection defines at least one volume(e.g., an intermediate process chamber 950 b) for containing a solidphase material for removal of ions and/or dyes from a sample material;providing biological sample material in one of the process chambers;transferring the biological sample material from one chamber to anotherchamber through the connection to allow the biological sample materialand solid phase material to remain in contact for a sufficient time toremove at least a portion of the ions and/or dyes from the biologicalsample material. Optionally, the solid phase material includes two ormore different types of particles. Optionally, the connection definestwo volumes, each containing a different solid phase material.

Alternative valve constructions that may be used in connection with thedevices and methods of the present invention are illustrated in FIGS.23A, 23B, 24A, 24B, 25A, and 25B. The valves may, for example, beconstructed, at least partially, of polymeric materials that exhibitshape memory effects. Some polymers that exhibit shape memory effect arediscussed in, e.g., U.S. Pat. Nos. 5,049,591 (Hayashi et al.); U.S. Pat.No. 5,128,197 (Kobayashi et al.); U.S. Pat. No. 5,135,786 (Hayashi etal.); U.S. Pat. No. 5,139,832 (Hayashi et al.); and U.S. Pat. No.5,145,935 (Hayashi). Many of these polymers are crosslinkedpolyurethanes. Other polymers, e.g., polynorbornene, may also exhibitshape memory effects.

In connection with polymeric materials, “shape memory effect” can begenerally described as involving the fabrication of a first structure ata temperature above the glass transition temperature (T_(g)) of thepolymer. That structure is then cooled below the T_(g) and deformed intoa second structure. When the polymer in the form of the second structureis heated above the T_(g), the polymer reverts to the first structure.

In addition to exhibiting shape memory effects, any polymeric materialsused in connection with the valves should be compatible with thereagents and other materials used in the devices and methods of thepresent invention. For example, where PCR is to be performed in devicesincorporating the shape memory polymer valves, the polymeric materialsin the valves are preferably compatible with the materials found in thePCR process.

Turning to FIGS. 23A and 23B, one valve structure that may be useful inconnection with the microfluidic devices and methods of the presentinvention is illustrated. The valve 1070 may be formed in the shape of acylinder when open as depicted in FIG. 23A and a pinched shape asillustrated in FIG. 23B when closed. The valve 1070 may be constructedto be normally open, i.e., open after manufacturing above the T_(g) ofthe polymeric material. As a result, the valve 1070 is closed (FIG. 23B)and then located in a device of the present invention until heated toabove the T_(g) of the shape memory effect polymer. Once heated abovethe T_(g) of the polymer, the valve 1070 reverts to its normally openstructure (FIG. 23A), thereby allowing materials to pass through thevalve 1070. Alternatively, the valve 1070 could be normally closed, suchthat heating would cause the valve 1070 to move from the open state(FIG. 23A) to the closed state (FIG. 23B).

Heating of the polymer may be achieved by any suitable technique,although it may be preferred to heat the polymer by non-contact heatingmethods. For example, the valve 1070 may be heated by electromagneticenergy (e.g., laser energy, RF energy, etc.). Alternatively, the polymermay be heated by conduction using resistance heaters, Peltier devices,etc. In another alternative, the valve 1070 may be heated by convectionusing, e.g., hot air or other heated fluids. Where a laser or othernon-contact source of energy is used, the polymeric material used toconstruct the valve 1070 may be impregnated or otherwise include one ormore materials that absorb electromagnetic energy of selectedwavelengths. For example, the polymeric material may be impregnated witha dye that absorbs laser energy (e.g., a dye that absorbs near infraredradiation, such as IR 792 perchlorate available from Aldrich Chemical).

Another valve structure 1170 is illustrated in FIGS. 24A and 24B. Thevalve 1170 is provided in the form of a film, e.g., a disc, asillustrated in FIG. 24A when constructed above the T_(g) of thepolymeric material, thus resulting a normally closed valve. Aftercooling to below the polymer's T_(g), the valve 1170 can be deformed tothe shape shown in FIG. 24B with an opening formed in the disc. When thevalve structure 1170 as seen in FIG. 24B is heated to a temperatureabove the T_(g) of the polymer, the valve will revert back to the shapedepicted in FIG. 24A, thus occluding the opening formed therein (as seenin FIG. 24B). Alternatively, the valve 1170 can be manufactured as anormally open valve.

Another alternative valve structure 1270 is depicted in FIGS. 25A and25B. The depicted valve structure 1270 may be located along a fluid path1262 (e.g., via or distribution channel). The valve structure 1270 maybe provided in the form of material located along the fluid path 1262.When heated above a selected temperature, the material of the valvestructure 1270 expands to close the fluid path 1262. The material usedin the valve structure 1270 may be, e.g., polymer that expands to form afoamed polymer. The foaming action may be provided, e.g., by using ablowing agent or supercritical carbon dioxide impregnation.

Where a blowing agent is used in the valve structure 1270, it may beimpregnated into the polymer. Examples of suitable blowing agents mayinclude, but are not limited to: CELOGEN AZ (available from UniroyalCorporation, Middlebury, Conn.), EXPANCEL microspheres (Expancel,Sweden), and glycidyl azide based polymers (available from MinnesotaMining and Manufacturing Company, St. Paul, Minn.). When the impregnatedpolymer is then heated above a selected temperature, the blowing agentgenerates a gas that causes the polymer to foam and expand and close thevalve structure 1270 as depicted in FIG. 25B.

Supercritical foaming may also be used to expand the valve structure1270. A polymer may be caused to foam by impregnating the polymer with,e.g., carbon dioxide, when the polymer is heated above its glasstransition temperature, with the impregnating occurring under highpressure. The carbon dioxide may be applied in liquid form to impregnatethe polymeric matrix. The impregnated material can be fabricated intothe valve structure, preferably in a compressed form. When heated thecarbon dioxide expands, the structure also expands, thereby closing thefluid path 1262.

Although not required, it may be possible to use a foamed shape memorypolymeric material to form the valve structure 1270, with the expansionof the foam enhancing the sealing effect of the valve structure 1270 onthe fluid path 1262.

In addition, it is possible to use a variant of the structure 1170depicted in FIG. 24B, wherein the material is shape memory foam preparedby the use of blowing agent or supercritical carbon dioxide gas, whichis then fabricated into the structure 1170. The application of heatcauses the structure to revert to that of FIG. 24A, with the expansionof the foam enhancing the sealing effect.

A seal system that exploits the characteristics of shape memorypolymeric materials is depicted in FIG. 26. The seal system may be usedto provide a resealable access port into, e.g., a process chamber 1350or other fluid structure on a device of the present invention. The sealsystem embodiment depicted in FIG. 26 includes an opening 1344 into aprocess chamber 1350, with the opening being closed by a seal 1346.

The seal 1346 is preferably provided in the form of a film, e.g., abarrier as depicted in FIG. 26, that is constructed above the T_(g) ofthe polymeric material, thus resulting a normally closed seal. The seal1346 can be pierced by a tool 1349 (e.g., a syringe needle) to eitherdeposit material in and/or remove material from the process chamber1350. The seal 1346 is thus deformed to include an opening formed in thedisc. When the seal 1346 is deformed while at a temperature below theT_(g) of the shape memory polymeric material, that opening can be closedby heating the seal 1346 to a temperature above the T_(g) of thepolymer, thus causing the seal 1346 to revert back to the shape depictedin FIG. 26 and closing the opening formed therein. The piercing andresealing of the seal 1346 may, in some instances be performed two ormore times if so desired.

FIGS. 27 and 28 depict another aspect of the sample processing methodsand systems of the present invention. This portion of the inventionaddresses the issue of removing residual reaction materials after, e.g.,Sanger cycling. Processes such as Sanger cycling may provide desiredreaction products along with residual materials such as unincorporateddye terminators.

When Sanger cycling is performed in the sample processing devices of thepresent invention, one potential technique for removing the unwantedmaterials (e.g., dyes) may involve the use of a solid phase materialsuch as paramagnetic particles. One example of suitable paramagneticparticles incorporating dye terminator removal materials is availableunder the tradename RAPXTRACT from Prolinx Inc., Bothell, Wash. Furtherexamples of these and similar materials (and their methods of use) maybe found in International Publication No. WO 01/25490 (titled: REMOVALOF DYE-LABELED DIDEOXY TERMINATORS FROM DNA SEQUENCING REACTIONS), andits priority documents (U.S. patent application Ser. Nos. 60/158,188;60/164,050; and 09/564,117), as well as in International Publication No.WO 01/25491 (titled: REMOVAL OF DYE-LABELED DIDEOXY TERMINATORS FROM DNASEQUENCING REACTIONS), and its priority documents (U.S. patentapplication Ser. Nos. 60/158,188; 60/164,050; and 09/564,117).

Referring to FIG. 27, one method of using paramagnetic particles inconnection with one sample processing device 1410 will be described.After loading the sample material into the loading chambers 1460, thedevice 1410 is rotated about axis 1412 to move the sample material tothe first set of process chambers 1450 a. The sample material may beprocessed in process chambers 1450 a by performing, e.g., PCR on thesample material. When processing is completed in the first processchambers 1450 a, valves 1470 a may be opened and the sample materialmoved to the second set of process chambers 1450 b by rotating thedevice 1410. A second process may be performed on the sample material inthe second process chambers 1450 b. In the method described herein, thesample material is Sanger cycled within the second process chambers 1450b to produce Sanger sequencing reaction products within the samplematerial. After Sanger cycling the sample material can be moved to theoutput chambers 1450 c by opening the valves 1470 b and rotating thedevice 1410.

Before delivery of the Sanger sequencing reaction products to the outputchambers 1450 c, however, it may be preferred to remove unwantedmaterials such as unincorporated dye terminators. To do so, paramagneticparticles including, e.g., dye terminator removal material may beintroduced into the loading chambers 1460, followed by rotating thedevice 1410 to move the paramagnetic particles out to the second processchambers 1450 b where the unincorporated dye terminators-may becaptured.

Movement of the paramagnetic particles through the device 1410 may befacilitated by locating a magnet proximate the device 1410. Referring toFIG. 28, a magnet 1490 may be located, e.g., above the device 1410, suchthat a magnetic field generated by the magnet extends through theprocess chambers as the device 1410 rotates about the axis 1412. As theparamagnetic particles are moved through the strongest portions of themagnetic field they are moved within the device 1410. The magneticforces may, therefore, prevent the particles from becoming packed intoany distribution channels or other smaller fluid pathways within thedevice 1410.

In addition, the magnetic forces may also facilitate mixing of theparamagnetic particles within any sample materials in which they arelocated. For example, it may be preferred to locate the magnet 1490 onthe opposite side of the device 1410 from the direction in which gravitypulls the paramagnetic particles. In another variation, two or moremagnets may be located on opposite sides of the device 1410 to provideopposing forces on the paramagnetic particles (with the magnets offsetaround the circumference of the device 1410). In either case, theparamagnetic particles may be subjected to forces pulling in oppositedirections intermittently. Additionally, it may be preferred to vary therotational speed of the device 1410 to further facilitate mixing of theparamagnetic particles in the process chambers.

After the paramagnetic particles have resided in the sample material fora sufficient period of time, they are preferably removed before thesample materials are sequenced. One preferred method of removing theparamagnetic particles is by filtering the sample material during, e.g.,moving the sample material from the second process chambers 1450 b tothe output chambers 1450 c. The paramagnetic particles may be filteredusing, e.g., filters located between the second process chambers 1450 band the output chambers 1450 c. Suitable filters may be in the form of,e.g., the porous plugs 670 described above in connection with FIG. 13.Another alternative filter may be the permeable supports 874 describedin connection with FIG. 19. As the device 1410 is rotated about axis,the sample material moves through the filter while the paramagneticparticles are prevented from moving on to the output chamber 1450 c.

Rather than moving the paramagnetic particles to the process chamberswhere they are need by rotating, it may be possible to locate theparamagnetic particles could be dried-down in the process chambers wherethey can be released when the sample material enters the processchamber. In another alternative, it may be possible to locate theparamagnetic particles in a porous membrane or plug such that theunincorporated dye terminator material can be extracted as the samplematerial moves through that structure.

FIGS. 29 & 30 depict a device structure and method that may facilitatemixing of sample material 1558 within a process chamber 1550. Samplematerial 1558 is delivered to the process chamber 1550 throughdistribution channel 1562 while rotating the device containing theprocess chamber 1550. The rotation preferably moves sample material 1558into the process chamber 1550 by centrifugal force. As discussed above,air or other fluids located within the process chamber 1550 beforedelivery of the sample material 1558 can be replaced by, e.g., varyingthe rotational speed of the device.

The process chamber 1550 includes an optional expansion chamber 1552that cannot be filled with sample material 1558 by rotation of thedevice containing the process chamber 1550. Filling of the expansionchamber 1552 with sample material 1558 can be prevented, for example, byproper positioning of the expansion chamber 1552 relative to the processchamber 1550. In the depicted embodiment, the expansion chamber 1552 isaligned with the distribution channel 1562 and, as a result, extendsfrom the process chamber 1550 generally back towards the axis ofrotation of the device.

Referring to FIG. 30, the sample material 1558 may be forced furtherinto the expansion chamber 1552 as its pressure increases duringacceleration of the device and move back out of the expansion chamber1552 as the pressure decreases when the rotational speed of the deviceis decreased. By alternately accelerating/decelerating the device,movement of the sample material 1558 into and out of the expansionchamber 1552 can be effected to enhance mixing of the sample material1558.

FIGS. 31 & 32 depict another potential feature that may be incorporatedinto sample processing devices of the present invention. In the figures,thermal isolation of a process chamber 1650 in the device can beenhanced by removing material around the process chamber 1650, with theprocess chamber 1650 being defined by a ring 1652 connected to thesurrounding body 1654 by one or more struts 1656. Essentially, theprocess chamber 1650 is surrounded by one or more voids. Channels todeliver sample materials to the process chamber 1650 or remove samplematerials from the process chamber 1650 can be located along the supportstruts 1654. Thermal isolation is improved by removing material aroundthe ring 1652 that could serve as a heat sink, drawing thermal energyaway from the process chamber 1650 during heating, or supplying storedthermal energy to the process chamber when cooling is desired.

As depicted, the cover layers 1630 and 1640 provided on both sides ofthe core 1620 may extend over the voids formed around the processchamber 1650, thereby providing a contained volume of air or otherinsulating material. Alternatively, one or both of the cover layers 1630and 1640 may be removed from around the ring 1652.

In addition to the enhanced thermal isolation of the suspended processchambers 1650, the suspended construction may offer improved complianceof the process chamber 1650 to a base plate or other structure on whichthe device may be placed. The improved compliance may be provided by thestruts

Turning to FIG. 33, another optional feature of devices according to thepresent invention is depicted. The device of FIGS. 31 & 32 is depictedas located on a base plate 1680 that includes raised protrusions 1682that are located beneath the process chambers 1650. It is preferred thatthe protrusions 1682 extend above the surrounding surface 1684 of thebase plate 1680.

The protrusions 1682 may enhance thermal transfer between the processchamber 1650 and base plate 1680 in a number of ways. When theprotrusions 1682 extend at least partially into the process chambers1650, they increase the surface area of the chamber 1650 that is exposedto the heated base plate 1680. In addition, by affirmatively engagingthe process chambers 1650, the protrusions 1682 may reduce or eliminateany air gaps between the process chambers 1650 and the base plate 1680in the area of the process chambers 1650. Such air gaps may insulate theprocess chambers 1650 from the base plate 1680, thereby degradingthermal transfer.

It may be preferred that the portions of the process chambers 1650 incontact with the protrusions 1680 exhibit sufficient compliance todeform in response to placement on the base plate 1680. For example, thecover layer 1640 may preferably include a deformable metallic foil. Inaddition, it may be preferred to provide the process chambers 1650 insuspended rings 1652 as described above with respect to FIGS. 31 & 32(which may offer improved compliance).

Further, it may be desirable to supply a force on the device 1610 inwhich process chambers 1650 are located to urge the device 1610 and baseplate 1680 towards each other. In some embodiments, the force may beprovided by a platen urging the device 1610 against the base plate 1680.In other embodiments, the device 1610 may be drawn towards the baseplate 1680 by, e.g., a spindle that extends through a central opening inthe device 1610 and draws the device 1610 towards base plate 1680. Otherstructures for providing a force urging the device 1610 and base plate1680 together will be known to those skilled in the art.

Patents, patent applications, and publications disclosed herein arehereby incorporated by reference (in their entirety) as if individuallyincorporated. It is to be understood that the above description isintended to be illustrative, and not restrictive. Various modificationsand alterations of this invention will become apparent to those skilledin the art from the foregoing description without departing from thescope of this invention, and it should be understood that this inventionis not to be unduly limited to the illustrative embodiments set forthherein.

1. A sample processing device comprising: a substrate that comprisesfirst and second major sides and a first cover attached to the firstmajor side of the substrate, wherein the first cover transmitselectromagnetic energy of selected wavelengths; a plurality of processchamber arrays formed in the substrate, each process chamber array ofthe plurality of process chamber arrays comprising a first chamberdefining a volume for containing sample material, a second chamberdefining a volume for containing sample material, a channel extendingbetween the first chamber and second chamber, wherein the plurality ofprocess chamber arrays are arranged radially on the substrate such thatthe second chamber is located radially outward of the first chamber ineach of the process chamber arrays; and a valve located in the channelbetween the first chamber and the second chamber in at least one processarray of the plurality of process arrays, wherein the valve comprises animpermeable membrane closing the channel, and wherein the valve isopened by forming a void through the impermeable membrane usingelectromagnetic energy passing through the first cover.
 2. A deviceaccording to claim 1, wherein the channel comprises a via formed in thesubstrate, the via comprising an opening at the first major side of thesubstrate, wherein the first cover extends over the opening, and whereinthe impermeable membrane is located within the via.
 3. A deviceaccording to claim 1, wherein the impermeable membrane is separate anddistinct from the substrate.
 4. A device according to claim 1, whereinthe impermeable membrane is molded integral with the substrate.
 5. Adevice according to claim 1, wherein the impermeable membrane comprisesa coating of material susceptible of absorbing at least some of theelectromagnetic energy of selected wavelengths transmitted by the firstcover and converting that electromagnetic energy to heat.
 6. A deviceaccording to claim 1, wherein the valve further comprises a permeablesupport proximate the impermeable membrane.
 7. A device according toclaim 1, wherein the channel comprises a via formed in the substrate,the via comprising an opening at the first major side of the substrate,wherein the first cover extends over the opening, and wherein theimpermeable membrane and the permeable support are both located withinthe via.
 8. A device according to claim 1, further comprising a secondcover attached to the second major surface of the substrate, wherein thesecond cover comprises metallic layer.
 9. A device according to claim 1,wherein the first cover is adhesively attached to the first major sideof the substrate.
 10. A device according to claim 1, wherein thesubstrate further comprises a top layer, a bottom layer, and a valvelayer located between the first layer and the second layer, wherein theimpermeable membrane of the valve in at least some process chamberarrays of the plurality of process chamber arrays comprises a portion ofthe valve layer.
 11. A device according to claim 10, wherein the valvelayer comprises material susceptible of absorbing at least some of theelectromagnetic energy of selected wavelengths transmitted by the firstcover and converting that electromagnetic energy to heat.
 12. A deviceaccording to claim 1, wherein the substrate further comprises a toplayer, a bottom layer, and a valve layer located between the first layerand the second layer, wherein the impermeable membrane of the valve allof the process chamber arrays of the plurality of process chamber arrayscomprises a portion of the valve layer.
 13. A device according to claim12, wherein the valve layer is coextensive with the top and bottomlayers of the substrate.
 14. A device according to claim 12, wherein thevalve layer comprises a coating of material susceptible of absorbing atleast some of the electromagnetic energy of selected wavelengthstransmitted by the first cover and converting that electromagneticenergy to heat.
 15. A sample processing device comprising: a substratethat comprises first and second major sides and a first cover attachedto the first major side of the substrate, wherein the first covertransmits electromagnetic energy of selected wavelengths; and aplurality of process chamber arrays formed in the substrate, eachprocess chamber array of the plurality of process chamber arrayscomprising a first chamber defining a volume for containing samplematerial, a second chamber defining a volume for containing samplematerial, and a channel extending between the first chamber and secondchamber, wherein the plurality of process chamber arrays are arrangedradially on the substrate such that the second chamber is locatedradially outward of the first chamber in each of the process chamberarrays; and a valve located in the channel between the first chamber andthe second chamber in at least two or more process chamber arrays of theplurality of process arrays, wherein the valve comprises an impermeablemembrane closing the channel, and wherein the valve is opened by forminga void through the impermeable membrane using electromagnetic energypassing through the first cover; wherein the channel comprises a viaformed in the substrate, the via comprising an opening at the firstmajor side of the substrate, wherein the first cover extends over theopening, and wherein the impermeable membrane is located within the via;and wherein the impermeable membrane comprises material susceptible ofabsorbing at least some of the electromagnetic energy of selectedwavelengths transmitted by the first cover and converting thatelectromagnetic energy to heat.
 16. A method of controlling fluid flowthrough a sample processing device, the method comprising: providing asample processing device comprising a substrate that comprises first andsecond major sides and a first cover attached to the first major side ofthe substrate, the sample processing device further comprising aplurality of process chamber arrays formed in the substrate, eachprocess chamber array of the plurality of process chamber arrayscomprising a first chamber defining a volume for containing samplematerial, a second chamber defining a volume for containing samplematerial, a channel extending between the first chamber and secondchamber, and a valve located in the channel between the first chamberand the second chamber, wherein the valve comprises an impermeablemembrane closing the channel; opening the valves in one or more of theprocess chamber arrays of the plurality of process chamber arrays bypassing electromagnetic energy of the selected wavelengths through thefirst cover, wherein the electromagnetic energy of selected wavelengthsforms a void through the impermeable membranes of the valves in the oneor more process chamber arrays; and rotating the sample processingdevice to pass fluid through the voids in the impermeable membranes ofthe valves in the one or more process chamber arrays.
 17. A methodaccording to claim 16, wherein the plurality of process chamber arraysare arranged radially with respect to an axis of rotation about whichthe substrate is rotated to pass fluid through the voids in theimpermeable membranes of the valves in the one or more process chamberarrays, wherein the second chamber is located radially outward of thefirst chamber in each of the process chamber arrays.
 18. A methodaccording to claim 16, wherein the impermeable membrane comprises acoating of material susceptible of absorbing at least some of theelectromagnetic energy of selected wavelengths.
 19. A method accordingto claim 16, wherein the impermeable membrane comprises materialsusceptible of absorbing at least some of the electromagnetic energy ofselected wavelengths, wherein the material is contained within theimpermeable membrane.
 20. A method according to claim 16, wherein thechannel in at least some of the process chamber arrays of the pluralityof process chamber arrays comprises a via formed in the substrate, thevia comprising an opening at the first major side of the substrate,wherein the first cover extends over the opening and the impermeablemembrane is located within the via, and wherein the method furthercomprises directing the electromagnetic energy of selected wavelengthsinto the vias.
 21. A method according to claim 16, wherein theelectromagnetic energy of selected wavelengths is emitted by a laser.22. A method of moving sample material within a sample processingdevice, the method comprising: providing a device comprising a pluralityof process chamber arrays, each process chamber array of the pluralityof process chamber arrays comprising a first process chamber, a secondprocess chamber, and a valve located between the first process chamberand the second process chamber, the valve comprising an impermeablebarrier; providing sample material in at least one process chamber arrayof the plurality of process chamber arrays, the sample material beingprovided in the first process chamber of the at least one processchamber array; placing the first process chamber of the at least oneprocess chamber array in fluid communication with the second processchamber of the at least one process chamber array by forming a void inthe impermeable barrier of the valve using electromagnetic energy ofselected wavelengths through a cover attached to a surface of thedevice; and moving the sample material from the first process chamber ofthe at least one process chamber array to the second process chamber inthe at least one process chamber array through the void by rotating thedevice.
 23. A method according to claim 22, wherein the plurality ofprocess chamber arrays are arranged radially with respect to an axis ofrotation about which the device is rotated to move the sample materialfrom the first process chamber of the at least one process chamber arrayto the second process chamber in the at least one process chamber array,wherein the second process chamber is located radially outward of thefirst process chamber in each of the process chamber arrays.
 24. Amethod according to claim 22, wherein the valve further comprises apermeable support member proximate the impermeable barrier.
 25. A methodaccording to claim 22, further comprising filtering the sample materialwhile moving the sample material from the first process chamber to thesecond process chamber in the at least one process chamber array.